http://www.nimblegen.com/news/events/webinar/index.html en-us 2011 Roche NimbleGen, Inc. Applications of the NimbleGen High-Definition Microarray Platform in Genomics Roche NimbleGen Inc. The Roche NimbleGen Webinar series features researchers describing their work incorporating NimbleGen microarrays in a diverse range of genomics and epigenomics research including the study of copy-number polymorphisms, the genome-wide mapping of DNA binding proteins, chromatin remodeling, histone and DNA methylation, gene expression analysis, and the identification and characterizaton of SNPs. The Roche NimbleGen Webinar Series is a forum for researchers to present their work on the leading edge of genomics. Learn how the creative efforts of prominant researchers, combined with the power of NimbleGen high-resolution, customizable oligonucleotide arrays, is is advancing our understanding at the nexus of regulatory biology and genomics. Roche NimbleGen, Inc. dmd.contact@roche.com clean Stephan Zuchner Dr. Zuchner discusses his research that recently identified a novel a novel Retinitis pigmentosa gene. Exome sequencing has become a mainstay for gene discovery in Mendelian diseases and beyond. However, genetically highly heterogeneous phenotypes still present challenging targets. An example is Retinitis pigmentosa (RP), a degenerative eye disease where greater than 50 known genes explain only approximately half of the affected families. When a new gene is implicated in RP, it is usually a relatively rare cause of the disease. This situation typically requires additional studies including classic chromosomal mapping, large-scale sequencing of unrelated probands, in silico analysis of protein function and pathways, and also rapid in vivo modeling of candidate sequence variants. This webinar will draw upon our extensive experience in exome sequencing and will detail our recent identification of a novel Retinitis pigmentosa gene, DHDDS, in a single nuclear family. http://www.nimblegen.com/news/events/webinar/podcasts/2011_08_18_exome_sequencing.mp3 Thu, 18 Aug 2011 16:00:00 GMT 00:39:12 seqcap, EZ, sequencing, enrichment, targeted re-sequencing, exome sequencing, NimbleGen, microarray, Roche, Retinitis pigmentosa Stephan Zuchner Dr. Zuchner discusses his research that recently identified a novel a novel Retinitis pigmentosa gene. Exome sequencing has become a mainstay for gene discovery in Mendelian diseases and beyond. However, genetically highly heterogeneous phenotypes still present challenging targets. An example is Retinitis pigmentosa (RP), a degenerative eye disease where greater than 50 known genes explain only approximately half of the affected families. When a new gene is implicated in RP, it is usually a relatively rare cause of the disease. This situation typically requires additional studies including classic chromosomal mapping, large-scale sequencing of unrelated probands, in silico analysis of protein function and pathways, and also rapid in vivo modeling of candidate sequence variants. This webinar will draw upon our extensive experience in exome sequencing and will detail our recent identification of a novel Retinitis pigmentosa gene, DHDDS, in a single nuclear family. http://www.nimblegen.com/news/events/webinar/podcasts/2011_08_18_exome_sequencing.m4v Thu, 18 Aug 2011 16:00:00 GMT 00:39:12 seqcap, EZ, sequencing, enrichment, targeted re-sequencing, exome sequencing, NimbleGen, microarray, Roche, Retinitis pigmentosa Marilou Wijdicks and Jeremy Lambert Roche NimbleGen and Caliper Life Sciences now provide a comprehensive high-throughput target enrichment solution. Recent collaborative efforts between Roche NimbleGen and Caliper Life Sciences have resulted in the development of an automated, optimized solution for large scale targeted resequencing sample preparation projects for Next Generation Sequencing. This webinar will demonstrate the advantages this integrated solution can provide to researchers who desire to increase throughput (up to 288 samples per week), enhance consistency, and minimize human errors in targeted resequencing projects. NimbleGen SeqCap EZ Library products enable researchers to reduce sequencing costs by allowing more samples to be multiplexed in a single sequencing run due to the combination of high capture efficiency and specificity. Learn how Roche NimbleGen and Caliper Life Sciences can enable the scale-up of your targeted resequencing sample preparation capabilities with minimal time and effort. http://www.nimblegen.com/news/events/webinar/podcasts/2011_08_11_seqcapez_automation.mp3 Thu, 11 Aug 2011 16:00:00 GMT 00:40:52 seqcap, EZ, sequencing, enrichment, targeted re-sequencing, exome sequencing, NimbleGen, microarray, Roche, automation, Caliper, Sciclone Marilou Wijdicks and Jeremy Lambert Roche NimbleGen and Caliper Life Sciences now provide a comprehensive high-throughput target enrichment solution. Recent collaborative efforts between Roche NimbleGen and Caliper Life Sciences have resulted in the development of an automated, optimized solution for large scale targeted resequencing sample preparation projects for Next Generation Sequencing. This webinar will demonstrate the advantages this integrated solution can provide to researchers who desire to increase throughput (up to 288 samples per week), enhance consistency, and minimize human errors in targeted resequencing projects. NimbleGen SeqCap EZ Library products enable researchers to reduce sequencing costs by allowing more samples to be multiplexed in a single sequencing run due to the combination of high capture efficiency and specificity. Learn how Roche NimbleGen and Caliper Life Sciences can enable the scale-up of your targeted resequencing sample preparation capabilities with minimal time and effort. http://www.nimblegen.com/news/events/webinar/podcasts/2011_08_11_seqcapez_automation.m4v Thu, 11 Aug 2011 16:00:00 GMT 00:40:52 seqcap, EZ, sequencing, enrichment, targeted re-sequencing, exome sequencing, NimbleGen, microarray, Roche, automation, Caliper, Sciclone Nadine Norton and Ray Hershberger Listen to Nadine and Ray's presentation on how they used Roche NimbleGen technology to identify BAG3 as a cause of DCM. Dilated cardiomyopathy (DCM), a common primary myocardial disease, causes systolic dysfunction and heart failure, a major public health problem. Its mode of transmission is mostly autosomal dominant but the disease is extremely heterogeneous with point mutations identified in over 30 genes. However, only ~35% of DCM genetic cause can be explained by point mutations in the known DCM genes, leaving most genetic cause unknown. In a multigenerational family with autosomal dominant transmission, we employed whole-exome sequencing in a proband and three of his affected family members, and genome-wide copy number variation in the proband and his affected father and unaffected mother. Exome sequencing identified 428 single point variants resulting in missense, nonsense, or splice site changes and 51 small insertion deletions; however, all were excluded based upon their presence in dbSNP, in-house population controls or their lack of segregation with those affected with DCM. Genome-wide copy number analysis using NimbleGen 2.1 M arrays identified 440 copy number variants > 1 kb, (median size ~13 kb). We then validated putative novel variants (not present in the database of genomic variants) with NimbleGen 135K custom arrays. Of these, a 8733 bp deletion, encompassing exon 4 of the heat shock protein cochaperone BCL2-associated athanogene 3 (BAG3), was found in seven affected family members and was absent in 355 controls. To establish the relevance of BAG3 rare variants in genetic DCM, we sequenced the coding exons in 311 other unrelated DCM probands and identified one frameshift, two nonsense, and four missense variants that were absent in over 967 exomes sequenced at Seattle Seq, four of which were familial and segregated with disease. Knockdown of bag3 in a zebrafish model recapitulated DCM and heart failure. We conclude that new comprehensive genomic approaches have identified rare variants in BAG3 as causative of DCM. http://www.nimblegen.com/news/events/webinar/podcasts/2011_06_30_norton_webinar.mp3 Thu, 30 Jun 2011 16:00:00 GMT 00:33:22 seqcap, EZ, sequencing, enrichment, targeted re-sequencing, exome sequencing, NimbleGen, microarray, Roche, DCM, BAG3, dilated cardiomyopathy, copy number variation, cnv, rare variants Nadine Norton and Ray Hershberger Watch Nadine and Ray's presentation on how they used Roche NimbleGen technology to identify BAG3 as a cause of DCM. Dilated cardiomyopathy (DCM), a common primary myocardial disease, causes systolic dysfunction and heart failure, a major public health problem. Its mode of transmission is mostly autosomal dominant but the disease is extremely heterogeneous with point mutations identified in over 30 genes. However, only ~35% of DCM genetic cause can be explained by point mutations in the known DCM genes, leaving most genetic cause unknown. In a multigenerational family with autosomal dominant transmission, we employed whole-exome sequencing in a proband and three of his affected family members, and genome-wide copy number variation in the proband and his affected father and unaffected mother. Exome sequencing identified 428 single point variants resulting in missense, nonsense, or splice site changes and 51 small insertion deletions; however, all were excluded based upon their presence in dbSNP, in-house population controls or their lack of segregation with those affected with DCM. Genome-wide copy number analysis using NimbleGen 2.1 M arrays identified 440 copy number variants > 1 kb, (median size ~13 kb). We then validated putative novel variants (not present in the database of genomic variants) with NimbleGen 135K custom arrays. Of these, a 8733 bp deletion, encompassing exon 4 of the heat shock protein cochaperone BCL2-associated athanogene 3 (BAG3), was found in seven affected family members and was absent in 355 controls. To establish the relevance of BAG3 rare variants in genetic DCM, we sequenced the coding exons in 311 other unrelated DCM probands and identified one frameshift, two nonsense, and four missense variants that were absent in over 967 exomes sequenced at Seattle Seq, four of which were familial and segregated with disease. Knockdown of bag3 in a zebrafish model recapitulated DCM and heart failure. We conclude that new comprehensive genomic approaches have identified rare variants in BAG3 as causative of DCM. http://www.nimblegen.com/news/events/webinar/podcasts/2011_06_30_norton_webinar.m4v Thu, 30 Jun 2011 16:00:00 GMT 00:33:21 seqcap, EZ, sequencing, enrichment, targeted re-sequencing, exome sequencing, NimbleGen, microarray, Roche, DCM, BAG3, dilated cardiomyopathy, copy number variation, cnv, rare variants Casey Matthews Listen to Casey's presentation on optimizing the next-generation sequencing pipeline with NimbleGen SeqCap EZ. From low throughput preparation of sample libraries to keeping the sequencing pipeline full, target enrichment and library preparation for next-generation sequencing has presented significant challenges at the Core Genotyping Facility at National Cancer Institute (NCI-CGF). Through key process optimization to library preparation coupled with the incorporation of NimbleGen SeqCap EZ, a solution-based enrichment technology, NCI-CGF has overcome the throughput challenges and increased capacity to manually enrich and process multiple 96-well plates. These improvements have proven to be significant, decreasing project turn-around times from one month to one week, opening the possibility of an automated solution, and decreasing costs while increasing efficiency for next generation targeted re-sequencing projects. Also presented in this webinar are target re-sequencing results from a genomic region associated with prostate cancer risk in 78 research samples. The results of this study have generated a detailed map of common genetic variations in chr19q13.33, and these variations should facilitate fine-mapping the association signal as well as determining the contribution of this locus to prostate cancer risk and regulation of prostate specific antigen (PSA) expression. http://www.nimblegen.com/news/events/webinar/podcasts/2010_05_06_seqcap_ez_webinar.mp3 Thu, 6 May 2010 17:00:00 GMT 00:52:07 seqcap, EZ, sequencing, enrichment, targeted re-sequencing, sequencing pipeline, NimbleGen, microarray, Roche Casey Matthews Watch Casey's presentation on optimizing the next-generation sequencing pipeline with NimbleGen SeqCap EZ. From low throughput preparation of sample libraries to keeping the sequencing pipeline full, target enrichment and library preparation for next-generation sequencing has presented significant challenges at the Core Genotyping Facility at National Cancer Institute (NCI-CGF). Through key process optimization to library preparation coupled with the incorporation of NimbleGen SeqCap EZ, a solution-based enrichment technology, NCI-CGF has overcome the throughput challenges and increased capacity to manually enrich and process multiple 96-well plates. These improvements have proven to be significant, decreasing project turn-around times from one month to one week, opening the possibility of an automated solution, and decreasing costs while increasing efficiency for next generation targeted re-sequencing projects. Also presented in this webinar are target re-sequencing results from a genomic region associated with prostate cancer risk in 78 research samples. The results of this study have generated a detailed map of common genetic variations in chr19q13.33, and these variations should facilitate fine-mapping the association signal as well as determining the contribution of this locus to prostate cancer risk and regulation of prostate specific antigen (PSA) expression. http://www.nimblegen.com/news/events/webinar/podcasts/2010_05_06_seqcap_ez_webinar.m4v Thu, 6 May 2010 17:00:00 GMT 00:52:08 seqcap, EZ, sequencing, enrichment, targeted re-sequencing, sequencing pipeline, NimbleGen, microarray, Roche Ken Lo Listen to Ken's presentation on the new NimbleGen 3x720K ChIP-chip and DNA Methylation arrays. Epigenetic changes in DNA methylation patterns and chromatin structure play key roles in the development of disease. Examples include Angelman and Prader-Willi syndromes, where epigenetic silencing is one factor in the development of these diseases. Therefore, understanding epigenetics is critical to our future understanding of many important diseases. Methods exist to analyze DNA methylation patterns in higher eukaryotes including methylated DNA immunoprecipitation-on-chip (MeDIP-chip), an affinity based approach to enrich methylated DNA regions from genomic DNA followed by microarray analysis. Similarly, chromatin structure and DNA-binding proteins can be mapped using chromatin immunoprecipitation-on-chip (ChIP-chip) using target protein specific antibodies and microarrays. Here we introduce our new Human, Mouse and Rat 3x720K ChIP-chip and DNA Methylation Arrays which offer comprehensive coverage of gene promoters and CpG islands in a multiplex platform. These arrays offer high resolution, 100bp probe spacing through all covered regions for highly sensitive and reproducible detection of DNA methylation and target protein DNA binding. In addition, the DNA methylation arrays also include probes covering positive, negative and nonCpG control regions to aid in assessment of the overall array performance. In this presentation, we will (1) describe the array designs and content in more detail, (2) demonstrate the sensitive and reproducible detection capabilities of these new arrays, and (3) compare the performance of these multiplex arrays with the single-plex 2.1M Deluxe Promoter arrays. http://www.nimblegen.com/news/events/webinar/podcasts/2010_02_18_epigenetics_webinar.mp3 Thu, 18 Feb 2010 17:00:00 GMT 00:53:50 chip-chip, methylation, DNA, epigenetic, MeDIP, CpG, NimbleGen, microarray, Roche Ken Lo Watch Ken's presentation on the new NimbleGen 3x720K ChIP-chip and DNA Methylation arrays. Epigenetic changes in DNA methylation patterns and chromatin structure play key roles in the development of disease. Examples include Angelman and Prader-Willi syndromes, where epigenetic silencing is one factor in the development of these diseases. Therefore, understanding epigenetics is critical to our future understanding of many important diseases. Methods exist to analyze DNA methylation patterns in higher eukaryotes including methylated DNA immunoprecipitation-on-chip (MeDIP-chip), an affinity based approach to enrich methylated DNA regions from genomic DNA followed by microarray analysis. Similarly, chromatin structure and DNA-binding proteins can be mapped using chromatin immunoprecipitation-on-chip (ChIP-chip) using target protein specific antibodies and microarrays. Here we introduce our new Human, Mouse and Rat 3x720K ChIP-chip and DNA Methylation Arrays which offer comprehensive coverage of gene promoters and CpG islands in a multiplex platform. These arrays offer high resolution, 100bp probe spacing through all covered regions for highly sensitive and reproducible detection of DNA methylation and target protein DNA binding. In addition, the DNA methylation arrays also include probes covering positive, negative and nonCpG control regions to aid in assessment of the overall array performance. In this presentation, we will (1) describe the array designs and content in more detail, (2) demonstrate the sensitive and reproducible detection capabilities of these new arrays, and (3) compare the performance of these multiplex arrays with the single-plex 2.1M Deluxe Promoter arrays. http://www.nimblegen.com/news/events/webinar/podcasts/2010_02_18_epigenetics_webinar.m4v Thu, 18 Feb 2010 17:00:00 GMT 00:54:12 chip-chip, methylation, DNA, epigenetic, MeDIP, CpG, NimbleGen, microarray, Roche Abigail Farfan Listen to Abigail's presentation to learn more about the features and performance of the MS 200 scanner. DNA Microarrays have become valuable tools for researchers in identifying biomarkers for active disease and assessing increased risk for certain genetic conditions. Roche NimbleGen, Inc. is a market leader in high-density DNA Microarrays with 2.1M probes per slide which, in a multiplex array format, provide an extremely high-quality, cost-effective, high-throughput solution for today’s microarray researcher. We proudly introduce the NimbleGen MS 200 Microarray Scanner for high resolution (down to 2 micron) scanning with a 48-slide autoloader and advanced automation capabilities that help ensure your high density arrays are analyzed with utmost precision and accuracy giving you consistent and robust data. The NimbleGen MS 200 is a state-of-the art DNA Microarray scanner optimized to provide excellent performance when used with NimbleGen arrays. With a completely isolated and ozone-protected slide magazine in addition to high-quality PMT detectors, the NimbleGen MS 200 provides the enhanced performance required to extract valuable data from even your most demanding microarray experiments. http://www.nimblegen.com/news/events/webinar/podcasts/2009_07_29_scanner_webinar.mp3 Wed, 29 Jul 2009 16:00:00 GMT 00:33:25 scanner, MS200, NimbleGen, microarray, Roche, DNA Abigail Farfan Watch Abigail's presentation to learn more about the features and performance of the MS 200 scanner. DNA Microarrays have become valuable tools for researchers in identifying biomarkers for active disease and assessing increased risk for certain genetic conditions. Roche NimbleGen, Inc. is a market leader in high-density DNA Microarrays with 2.1M probes per slide which, in a multiplex array format, provide an extremely high-quality, cost-effective, high-throughput solution for today’s microarray researcher. We proudly introduce the NimbleGen MS 200 Microarray Scanner for high resolution (down to 2 micron) scanning with a 48-slide autoloader and advanced automation capabilities that help ensure your high density arrays are analyzed with utmost precision and accuracy giving you consistent and robust data. The NimbleGen MS 200 is a state-of-the art DNA Microarray scanner optimized to provide excellent performance when used with NimbleGen arrays. With a completely isolated and ozone-protected slide magazine in addition to high-quality PMT detectors, the NimbleGen MS 200 provides the enhanced performance required to extract valuable data from even your most demanding microarray experiments. http://www.nimblegen.com/news/events/webinar/podcasts/2009_07_29_scanner_webinar.m4v Wed, 29 Jul 2009 16:00:00 GMT 00:33:29 scanner, MS200, NimbleGen, microarray, Roche, DNA Andrew Sharp Hear Andy's presentation on identifying novel imprinted genes by methylation profiling. One of the major features associated with imprinting is the presence of parent-of-origin specific Differentially Methylated Regions (DMRs). Thus, the maternal and paternal genomes possess distinct epigenetic marks which distinguish them at imprinted loci. In order to construct an imprinting map of the human genome, we have profiled DNA methylation patterns genome-wide in rare uniparental tissues. For genome-wide studies, we have compared methylation patterns in a panel of complete hydatidiform moles, which have an exclusively paternal genetic contribution, and ovarian teratomas, which have an exclusively maternal genetic contribution. Methylated DNA was immunoprecipitated using anti 5-methyl cytidine and hybridized to Nimblegen high-density oligonucleotide tiling arrays composed of 21 million probes distributed throughout the genome, generating complete profiles of the maternal and paternal methylomes. Comparison of these profiles identifies numerous sites of methylation difference, including sites of methylation polymorphism, novel imprinted loci, and also tissue specific differences. Examination of known imprinted genes showed that many are associated with DMRs, validating this as a system for the detection of imprinting. Many novel putative imprinted loci on nearly every human chromosome were also identified. These include novel DMRs within known imprinted gene clusters, as well as chromosomal regions not previously thought to be imprinted. In order to identify novel imprinted genes specifically on chromosome 15, we have also profiled DNA methylation in cases with uniparental disomy of chromosome 15 (UPD15). Comparison of six individuals with maternal versus paternal UPD15 reveals fourteen DMRs on chromosome 15. Some novel DMRs are located outside of 15q11-q13, and are associated with genes not previously thought to be imprinted, including IGF1R at 15q26.3, which plays a fundamental role in growth regulation. To validate our array data we performed bisulfite sequencing of putative DMRs, giving base-pair resolution of these imprints and confirming the presence of parent-of-origin specific methylation marks in multiple independent samples. Our data provides the first imprinting map of the human genome, demonstrates that the number of imprinted loci in the human genome is much higher than previously thought, and suggests that imprinting may influence the phenotypes of many human diseases. http://www.nimblegen.com/news/events/webinar/podcasts/2009_06_18_methylation_webinar.mp3 Thu, 18 Jun 2009 11:00:00 CDT 00:59:47 methylation, DNA, epigenetic, MeDIP, CpG, NimbleGen, microarray, Roche Andrew Sharp One of the major features associated with imprinting is the presence of parent-of-origin specific Differentially Methylated Regions (DMRs). Thus, the maternal and paternal genomes possess distinct epigenetic marks which distinguish them at imprinted loci. In order to construct an imprinting map of the human genome, we have profiled DNA methylation patterns genome-wide in rare uniparental tissues. For genome-wide studies, we have compared methylation patterns in a panel of complete hydatidiform moles, which have an exclusively paternal genetic contribution, and ovarian teratomas, which have an exclusively maternal genetic contribution. Methylated DNA was immunoprecipitated using anti 5-methyl cytidine and hybridized to Nimblegen high-density oligonucleotide tiling arrays composed of 21 million probes distributed throughout the genome, generating complete profiles of the maternal and paternal methylomes. Comparison of these profiles identifies numerous sites of methylation difference, including sites of methylation polymorphism, novel imprinted loci, and also tissue specific differences. Examination of known imprinted genes showed that many are associated with DMRs, validating this as a system for the detection of imprinting. Many novel putative imprinted loci on nearly every human chromosome were also identified. These include novel DMRs within known imprinted gene clusters, as well as chromosomal regions not previously thought to be imprinted. In order to identify novel imprinted genes specifically on chromosome 15, we have also profiled DNA methylation in cases with uniparental disomy of chromosome 15 (UPD15). Comparison of six individuals with maternal versus paternal UPD15 reveals fourteen DMRs on chromosome 15. Some novel DMRs are located outside of 15q11-q13, and are associated with genes not previously thought to be imprinted, including IGF1R at 15q26.3, which plays a fundamental role in growth regulation. To validate our array data we performed bisulfite sequencing of putative DMRs, giving base-pair resolution of these imprints and confirming the presence of parent-of-origin specific methylation marks in multiple independent samples. Our data provides the first imprinting map of the human genome, demonstrates that the number of imprinted loci in the human genome is much higher than previously thought, and suggests that imprinting may influence the phenotypes of many human diseases. Watch Andy's presentation on identifying novel imprinted genes by methylation profiling. http://www.nimblegen.com/news/events/webinar/podcasts/2009_06_18_methylation_webinar.m4v Thu, 18 Jun 2009 11:00:00 CDT 00:59:49 methylation, DNA, epigenetic, MeDIP, CpG, NimbleGen, microarray, Roche Andrew Sharp Hear Andy's presentation on DNA Methylation from the Roche NimbleGen workshop at the ESHG 2009 Annual Meeting in Vienna, Austria. http://www.nimblegen.com/news/events/webinar/podcasts/eshg_2009_sharp.mp3 Mon, 25 May 2009 11:45:00 GMT 00:20:46 methylation, DNA, epigenetic, MeDIP, CpG, NimbleGen, microarray, Roche Andrew Sharp Watch Andy's presentation on DNA Methylation from the Roche NimbleGen workshop at the ESHG 2009 Annual Meeting in Vienna, Austria. http://www.nimblegen.com/news/events/webinar/podcasts/eshg_2009_sharp.m4v Mon, 25 May 2009 11:45:00 GMT 00:20:47 methylation, DNA, epigenetic, MeDIP, CpG, NimbleGen, microarray, Roche Alistair Reid Hear Alistair's presentation on CGH from the Roche NimbleGen workshop at the ESHG 2009 Annual Meeting in Vienna, Austria. http://www.nimblegen.com/news/events/webinar/podcasts/eshg_2009_reid.mp3 Mon, 25 May 2009 11:15:00 GMT 00:20:23 NimbleGen, CGH, microarray, copy-number variants, CNV, PAG, Roche Alistair Reid Watch Alistair's presentation on CGH from the Roche NimbleGen workshop at the ESHG 2009 Annual Meeting in Vienna, Austria. http://www.nimblegen.com/news/events/webinar/podcasts/eshg_2009_reid.m4v Mon, 25 May 2009 11:15:00 GMT 00:20:25 NimbleGen, CGH, microarray, copy-number variants, CNV, PAG, Roche A. Leonardo Iniguez Hear Leo's presentation on the NimbleGen 2.1M DNA Methylation Arrays. http://www.nimblegen.com/news/events/webinar/podcasts/2009_04_09_methylation_webinar.mp3 Thu, 9 Apr 2009 11:00:00 CDT 01:02:54 methylation, DNA, epigenetic, MeDIP, CpG, NimbleGen, microarray, Roche A. Leonardo Iniguez Watch Leo's presentation on the NimbleGen 2.1M DNA Methylation Arrays. http://www.nimblegen.com/news/events/webinar/podcasts/2009_04_09_methylation_webinar.m4v Thu, 9 Apr 2009 11:00:00 CDT 01:02:56 methylation, DNA, epigenetic, MeDIP, CpG, NimbleGen, microarray, Roche Dan Burgess Hear Dan Burgess's presentation on the NimbleGen Sequence Capture 2.1M Human Exome Array. http://www.nimblegen.com/news/events/webinar/podcasts/burgess.mp3 Thu, 15 Jan 2009 11:00:00 CDT 00:59:20 sequencing, NimbleGen, 454, microarray, sequence capture, DNA, PCR, Roche, exome Dan Burgess Watch Dan Burgess's presentation on the NimbleGen Sequence Capture 2.1M Human Exome Array. http://www.nimblegen.com/news/events/webinar/podcasts/burgess.m4v Thu, 15 Jan 2009 11:00:00 CDT 00:59:26 sequencing, NimbleGen, 454, microarray, sequence capture, DNA, PCR, Roche, exome Nathan Springer Hear Nathans's presentation on sequence capture from the Roche NimbleGen workshop at the PAG 2009 Annual Meeting in San Diego, USA. http://www.nimblegen.com/news/events/webinar/podcasts/pag_2009_springer.mp3 Tue, 13 Jan 2009 19:30:00 PST 00:26:08 sequencing, NimbleGen, 454, microarray, sequence capture, DNA, PAG, Roche Nathan Springer Watch Nathans's presentation on sequence capture from the Roche NimbleGen workshop at the PAG 2009 Annual Meeting in San Diego, USA. http://www.nimblegen.com/news/events/webinar/podcasts/pag_2009_springer.m4v Tue, 13 Jan 2009 19:30:00 PST 00:26:08 sequencing, NimbleGen, 454, microarray, sequence capture, DNA, PAG, Roche Carlos Alvarez Hear Carlos' presentation on copy number variation from the Roche NimbleGen workshop at the PAG 2009 Annual Meeting in San Diego, USA. http://www.nimblegen.com/news/events/webinar/podcasts/pag_2009_alvarez.mp3 Tue, 13 Jan 2009 19:00:00 PST 00:21:28 NimbleGen, CGH, microarray, copy-number variants, CNV, PAG, Roche Carlos Alvarez Watch Carlos' presentation on copy number variation from the Roche NimbleGen workshop at the PAG 2009 Annual Meeting in San Diego, USA. http://www.nimblegen.com/news/events/webinar/podcasts/pag_2009_alvarez.m4v Tue, 13 Jan 2009 19:00:00 PST 00:21:30 NimbleGen, CGH, microarray, copy-number variants, CNV, PAG, Roche Scott Selleck Hear Scott's presentation on genomic copy number variant analysis from the Roche NimbleGen workshop at the ASHG 2008 Annual Meeting in Phildelphia, USA. http://www.nimblegen.com/news/events/webinar/podcasts/ashg_2008_selleck.mp3 Wed, 12 Nov 2008 19:30:00 CDT 00:35:14 NimbleGen, CGH, microarray, copy-number variants, CNV, Philadelphia, ASHG, Roche Scott Selleck Watch Scott's presentation on genomic copy number variant analysis from the Roche NimbleGen workshop at the ASHG 2008 Annual Meeting in Phildelphia, USA. http://www.nimblegen.com/news/events/webinar/podcasts/ashg_2008_selleck.m4v Wed, 12 Nov 2008 19:30:00 CDT 00:35:15 NimbleGen, CGH, microarray, copy-number variants, CNV, Philadelphia, ASHG, Roche David Hawkins Hear David's presentation on DNA methyation analysis from the Roche NimbleGen workshop at the ASHG 2008 Annual Meeting in Phildelphia, USA. http://www.nimblegen.com/news/events/webinar/podcasts/ashg_2008_hawkins.mp3 Wed, 12 Nov 2008 20:00:00 CDT 00:23:55 DNA methylation, NimbleGen, microarray, methyome, ASHG, Philadelphia, Roche David Hawkins Watch David's presentation on DNA methyation analysis from the Roche NimbleGen workshop at the ASHG 2008 Annual Meeting in Phildelphia, USA. http://www.nimblegen.com/news/events/webinar/podcasts/ashg_2008_hawkins.m4v Wed, 12 Nov 2008 20:00:00 CDT 00:23:55 DNA methylation, NimbleGen, microarray, methyome, ASHG, Philadelphia, Roche Matthew Bainbridge Hear Matthew's presentation on sequence capture for high-throughput sequencing from the Roche NimbleGen workshop at the ASHG 2008 Annual Meeting in Phildelphia, USA. http://www.nimblegen.com/news/events/webinar/podcasts/ashg_2008_bainbridge.mp3 Wed, 12 Nov 2008 20:30:00 CDT 00:19:15 sequencing, NimbleGen, 454, microarray, sequence capture, DNA, PCR, Roche, ASHG, Philadelphia Matthew Bainbridge Watch Matthew's presentation on sequence capture for high-throughput sequencing from the Roche NimbleGen workshop at the ASHG 2008 Annual Meeting in Phildelphia, USA. http://www.nimblegen.com/news/events/webinar/podcasts/ashg_2008_bainbridge.m4v Wed, 12 Nov 2008 20:30:00 CDT 00:19:16 sequencing, NimbleGen, 454, microarray, sequence capture, DNA, PCR, Roche, ASHG, Philadelphia Leo Iniguez Hear Leo Iniguez's presentation on introducing NimbleGen HD2 Arrays for high-resolution ChIP-chip analysis. http://www.nimblegen.com/news/events/webinar/podcasts/iniguez.mp3 Thu, 6 Nov 2008 11:00:00 CDT 00:54:44 Tiling expression, ChIP, non-coding, transcription, regulation, NimbleGen, gene expression, microarray, genomics, DNA Leo Iniguez Watch Leo Iniguez's presentation on introducing NimbleGen HD2 Arrays for high-resolution ChIP-chip analysis. http://www.nimblegen.com/news/events/webinar/podcasts/iniguez.m4v Thu, 6 Nov 2008 11:00:00 CDT 00:55:10 Tiling expression, ChIP, non-coding, transcription, regulation, NimbleGen, gene expression, microarray, genomics, DNA Stephan Beck Hear Stephan's presentation on DNA methyation analysis from the Roche NimbleGen workshop at the ESHG 2008 Annual Meeting in Barcelona, Spain. http://www.nimblegen.com/news/events/webinar/podcasts/beck_eshg.mp3 Mon, 2 Jun 2008 20:00:00 CDT 00:28:17 DNA methylation, NimbleGen, microarray, methyome, ESHG, Barcelona, Roche Stephan Beck Watch Stephan's presentation on DNA methyation analysis from the Roche NimbleGen workshop at the ESHG 2008 Annual Meeting in Barcelona, Spain. http://www.nimblegen.com/news/events/webinar/podcasts/beck.m4v Mon, 2 Jun 2008 20:00:00 CDT 00:28:19 DNA methylation, NimbleGen, microarray, methyome, ESHG, Barcelona, Roche Daniel Turner Hear Daniel's presentation on sequence capture for high-throughput sequencing from the Roche NimbleGen workshop at the ESHG 2008 Annual Meeting in Barcelona, Spain. http://www.nimblegen.com/news/events/webinar/podcasts/turner_eshg.mp3 Mon, 2 Jun 2008 20:00:00 CDT 00:18:14 sequencing, NimbleGen, 454, microarray, sequence capture, DNA, PCR, Roche, ESHG, Barcelona Daniel Turner Watch Daniel's presentation on sequence capture for high-throughput sequencing from the Roche NimbleGen workshop at the ESHG 2008 Annual Meeting in Barcelona, Spain. http://www.nimblegen.com/news/events/webinar/podcasts/turner.m4v Mon, 2 Jun 2008 20:00:00 CDT 00:18:15 sequencing, NimbleGen, 454, microarray, sequence capture, DNA, PCR, Roche, ESHG, Barcelona Tom Albert Hear Tom Albert's presentation on NimbleGen Sequence Capture Technology for targeted enrichment of selected genomic regions for next-gen sequencing. http://www.nimblegen.com/news/events/webinar/podcasts/albert.mp3 Thu, 3 Apr 2008 11:00:00 CDT 00:52:45 sequencing, NimbleGen, 454, microarray, sequence capture, DNA, PCR, Roche Tom Albert Watch Tom Albert's presentation on NimbleGen Sequence Capture Technology for targeted enrichment of selected genomic regions for next-gen sequencing. http://www.nimblegen.com/news/events/webinar/podcasts/albert.m4v Thu, 3 Apr 2008 11:00:00 CDT 00:47:59 sequencing, NimbleGen, 454, microarray, sequence capture, DNA, PCR, Roche Matt Gamble Hear Matt Gamble's presentation on the integrated use of NimbleGen epigenetic analysis tools in the functional analysis of PARP-1 and its interplay with Histone H1. http://www.nimblegen.com/news/events/webinar/podcasts/gamble.mp3 Wed, 19 Mar 2008 11:00:00 CDT 00:43:20 epigenetic, NimbleGen, ChIP, microarray, PARP, DNA, histone, Roche Matt Gamble Watch Matt Gamble's presentation on the integrated use of NimbleGen epigenetic analysis tools in the functional analysis of PARP-1 and its interplay with Histone H1. http://www.nimblegen.com/news/events/webinar/podcasts/gamble.m4v Wed, 19 Mar 2008 11:00:00 CDT 00:43:22 epigenetic, NimbleGen, ChIP, microarray, PARP, DNA, histone, Roche Janine LaSalle Hear Janine LaSalle's presentation on the integrated use of NimbleGen genomic and epigenomic tools in the functional analysis of methyl CpG binding protein 2, a key protein in Rett syndrome. http://www.nimblegen.com/news/events/webinar/podcasts/lasalle.mp3 Thu, 28 Feb 2008 11:00:00 CDT 01:00:59 epigenetic, NimbleGen, ChIP, microarray, MeCP2, DNA, histone, Roche Janine LaSalle Watch Janine LaSalle's presentation on the integrated use of NimbleGen genomic and epigenomic tools in the functional analysis of methyl CpG binding protein 2, a key protein in Rett syndrome. http://www.nimblegen.com/news/events/webinar/podcasts/lasalle.m4v Thu, 28 Feb 2008 11:00:00 CDT 01:00:09 epigenetic, NimbleGen, ChIP, microarray, MeCP2, DNA, histone, Roche Xinmin Zhang Hear Xinmin Zhang's presentation at PAG 2008 on the use of NimbleGen microarrays for the direct selection of thousands of genomic exons or loci for high-throughput sequencing http://www.nimblegen.com/news/events/webinar/podcasts/pag_xinmin.mp3 Sat, 16 Feb 2008 11:00:00 CDT 00:26:07 genetics, NimbleGen, DNA sequencing, microarray, tiling, DNA, 454, Roche Xinmin Zhang Watch Xinmin Zhang's presentation at PAG 2008 on the use of NimbleGen microarrays for the direct selection of thousands of genomic exons or loci for high-throughput sequencing http://www.nimblegen.com/news/events/webinar/podcasts/pag_xinmin.m4v Sat, 16 Feb 2008 11:00:00 CDT 00:26:08 genetics, NimbleGen, DNA sequencing, microarray, tiling, DNA, 454, Roche Steve DiFazio Hear Steve DiFazio's presentation at PAG 2008 on the use of NimbleGen microarrays for analysis of genome duplications in the Populus genome http://www.nimblegen.com/news/events/webinar/podcasts/pag_difazio.mp3 Sat, 16 Feb 2008 11:00:00 CDT 00:25:00 genetics, NimbleGen, DNA, populus, genome duplication, expression, DNA, Roche Steve DiFazio Watch Steve DiFazio's presentation at PAG 2008 on the use of NimbleGen microarrays for analysis of genome duplications in the Populus genome http://www.nimblegen.com/news/events/webinar/podcasts/pag_difazio.m4v Sat, 16 Feb 2008 11:00:00 CDT 00:25:00 genetics, NimbleGen, DNA, populus, genome duplication, expression, DNA, Roche Lex Flagel Hear Lex Flagel's presentation at PAG 2008 on the use of NimbleGen microarrays for analysis of duplicate gene expression in cotton http://www.nimblegen.com/news/events/webinar/podcasts/pag_flagel.mp3 Sat, 16 Feb 2008 11:00:00 CDT 00:27:13 genetics, NimbleGen, DNA, cotton, genome duplication, expression, DNA, Roche Lex Flagel Watch Lex Flagel's presentation at PAG 2008 on the use of NimbleGen microarrays for analysis of duplicate gene expression in cotton http://www.nimblegen.com/news/events/webinar/podcasts/pag_flagel.m4v Sat, 16 Feb 2008 11:00:00 CDT 00:27:13 genetics, NimbleGen, DNA, cotton, genome duplication, expression, DNA, Roche Roche NimbleGen Hear the entire Roche NimbleGen workshop presentation from PAG 2008 http://www.nimblegen.com/news/events/webinar/podcasts/pag_2008.mp3 Sat, 16 Feb 2008 11:00:00 CDT 01:26:11 genetics, NimbleGen, DNA, cotton, genome duplication, expression, populus, sequencing, 454, DNA, Roche Roche NimbleGen Watch the entire Roche NimbleGen workshop presentation from PAG 2008 http://www.nimblegen.com/news/events/webinar/podcasts/pag_2008.m4v Sat, 16 Feb 2008 11:00:00 CDT 01:18:21 genetics, NimbleGen, DNA, cotton, genome duplication, expression, populus, sequencing, 454, DNA, Roche Heather Mefford Hear Heather Meffords presentation on the use on the use of NimbleGen aCGH in the analysis of chromosomal rearrangements in human developmental disorders and disease. Genomic disorders are conditions that result from recurrent rearrangement of DNA caused by unequal crossing over between duplicated genomic sequences. Most studies of genomic disorders have focused on patients with cognitive disability and/or peripheral nervous system defects. In an effort to broaden the phenotypic spectrum of this disease model, we assessed 155 autopsy samples from fetuses with well-defined developmental pathologies in regions predisposed to recurrent rearrangement by array CGH. We found that 6% of fetal material showed evidence of microdeletion or microduplication, One of the microdeletions, identified in a fetus with multicystic dysplastic kidneys, encompasses the TCF2 gene on 17q12, previously shown to be mutated in maturity-onset diabetes as well as a subset of pediatric renal abnormalities. Fine-scale mapping with custom oligonucleotide arrays of the breakpoints in different patient cohorts reveals a recurrent 1.5 Mb de novo deletion in individuals with phenotypes ranging from congenital renal abnormalities to maturity-onset diabetes of the young type 5. Array analysis also reveals significant copy number and structural variation at the breakpoints. The 17q12 microdeletion is the first genomic disorder associated with diabetes and accounts for a significant proportion of previously unexplained pediatric renal disease. http://www.nimblegen.com/news/events/webinar/podcasts/mefford.mp3 Thu, 29 Nov 2007 11:00:00 CDT 00:52:46 genetics, NimbleGen, copy number variation, CGH, microarray, tiling, DNA, diabetes, developmental disorder, segmental duplication, Roche Heather Mefford Watch Heather Meffords presentation on the use on the use of NimbleGen aCGH in the analysis of chromosomal rearrangements in human developmental disorders and disease. Genomic disorders are conditions that result from recurrent rearrangement of DNA caused by unequal crossing over between duplicated genomic sequences. Most studies of genomic disorders have focused on patients with cognitive disability and/or peripheral nervous system defects. In an effort to broaden the phenotypic spectrum of this disease model, we assessed 155 autopsy samples from fetuses with well-defined developmental pathologies in regions predisposed to recurrent rearrangement by array CGH. We found that 6% of fetal material showed evidence of microdeletion or microduplication, One of the microdeletions, identified in a fetus with multicystic dysplastic kidneys, encompasses the TCF2 gene on 17q12, previously shown to be mutated in maturity-onset diabetes as well as a subset of pediatric renal abnormalities. Fine-scale mapping with custom oligonucleotide arrays of the breakpoints in different patient cohorts reveals a recurrent 1.5 Mb de novo deletion in individuals with phenotypes ranging from congenital renal abnormalities to maturity-onset diabetes of the young type 5. Array analysis also reveals significant copy number and structural variation at the breakpoints. The 17q12 microdeletion is the first genomic disorder associated with diabetes and accounts for a significant proportion of previously unexplained pediatric renal disease. http://www.nimblegen.com/news/events/webinar/podcasts/mefford.m4v Thu, 29 Nov 2007 11:00:00 CDT 00:52:37 genetics, NimbleGen, copy number variation, CGH, microarray, tiling, DNA, diabetes, developmental disorder, segmental duplication, Roche Henriette O'Geen Hear Henny's presentation on the use of NimbleGen ChIP-chip microarrays to analyze the binding patterns of the corepressor KAP1. Methylation of lysine residues on histone H3 and H4 tails plays a key role in gene regulation, chromatin structure, and establishment and maintenance of epigenetic memory. In particular, methylation of lysines 9 or 27 of histone H3 (H3me3K9 and H3me3K27, respectively) have been associated with silenced chromatin. ChIP-chip analysis using human promoter arrays indicate that the two marks segregate differentially with the two most common types of transcription factors; H3me3K9 is highly enriched at zinc finger genes (ZNFs) and H3me3K27 is highly enriched at homeobox genes. Here we show that many promoters containing the H3me3K9 mark are also bound by the corepressor KAP1 (also known as TIF1B or TRIM28). We then performed a complete genomic analysis using a set of 38 tiling arrays, which identified ~7000 KAP1 binding sites in the entire human genome. KAP1 binding was specifically enriched at zinc finger genes. Although most KAP1 binding sites were within core promoter regions, a unique binding pattern was observed at ZNF target genes. Analysis of ChIP-chip data from promoter arrays as well as from whole genome tiling arrays will be discussed. http://www.nimblegen.com/news/events/webinar/podcasts/ogeen.mp3 Thu, 1 Nov 2007 11:00:00 CDT 00:54:41 ChIP, chromatin, histone, immunoprecipitation, transcription, DNA, microarray Henriette O'Geen Watch Henny's presentation on the use of NimbleGen ChIP-chip microarrays to analyze the binding patterns of the corepressor KAP1. Methylation of lysine residues on histone H3 and H4 tails plays a key role in gene regulation, chromatin structure, and establishment and maintenance of epigenetic memory. In particular, methylation of lysines 9 or 27 of histone H3 (H3me3K9 and H3me3K27, respectively) have been associated with silenced chromatin. ChIP-chip analysis using human promoter arrays indicate that the two marks segregate differentially with the two most common types of transcription factors; H3me3K9 is highly enriched at zinc finger genes (ZNFs) and H3me3K27 is highly enriched at homeobox genes. Here we show that many promoters containing the H3me3K9 mark are also bound by the corepressor KAP1 (also known as TIF1B or TRIM28). We then performed a complete genomic analysis using a set of 38 tiling arrays, which identified ~7000 KAP1 binding sites in the entire human genome. KAP1 binding was specifically enriched at zinc finger genes. Although most KAP1 binding sites were within core promoter regions, a unique binding pattern was observed at ZNF target genes. Analysis of ChIP-chip data from promoter arrays as well as from whole genome tiling arrays will be discussed. http://www.nimblegen.com/news/events/webinar/podcasts/ogeen.m4v Thu, 1 Nov 2007 11:00:00 CDT 00:54:43 ChIP, chromatin, histone, immunoprecipitation, transcription, DNA, microarray Dr. Jonathan Sebat, Cold Spring Harbor Laboratory Hear the audio of Jonathan's presentation on de novo copy number variation in autism from the Roche NimbleGen Genetics and Epigenetics Workshop at ASHG, 2007 in San Diego, CA New methods for detecting changes in DNA copy number (CNVs) have begun to shed new light on genetic risk factors for Autism Spectrum Disorders. What these studies have shown is that large scale deletions and duplications of gene are a significant contributor to genetic risk, and furthermore that CNV risk factors are frequently the result of spontaneous germline mutation. Our findings raise the hypothesis that much the sporadic nature of autism due to spontaneous mutations. Spontaneous CNVs have been detected at many loci throughout the genome, and no single locus has been shown to account more than 1% of cases. These data are consistent with the notion that there are many genes in the genome that, when altered, can produce a similar disease phenotype. We hypothesize that the features of autism (impaired social interaction, difficulty with communication, and restricted interests and behaviors) owe there "commonality" to the fact that the diverse set of genes involved participate in a common biological network. http://www.nimblegen.com/news/events/webinar/podcasts/sebat.mp3 Thu, 25 Oct 2007 18:30:00 PDT 00:36:00 autism, CNVs, copy number variation, ROMA, aCGH, comparative genomic hybridization, microarray, genomics, DNA Dr. Jonathan Sebat, Cold Spring Harbor Laboratory Watch the video of Jonathan's presentation on de novo copy number variation in autism from the Roche NimbleGen Genetics and Epigenetics Workshop at ASHG, 2007 in San Diego, CA New methods for detecting changes in DNA copy number (CNVs) have begun to shed new light on genetic risk factors for Autism Spectrum Disorders. What these studies have shown is that large scale deletions and duplications of gene are a significant contributor to genetic risk, and furthermore that CNV risk factors are frequently the result of spontaneous germline mutation. Our findings raise the hypothesis that much the sporadic nature of autism due to spontaneous mutations. Spontaneous CNVs have been detected at many loci throughout the genome, and no single locus has been shown to account more than 1% of cases. These data are consistent with the notion that there are many genes in the genome that, when altered, can produce a similar disease phenotype. We hypothesize that the features of autism (impaired social interaction, difficulty with communication, and restricted interests and behaviors) owe there "commonality" to the fact that the diverse set of genes involved participate in a common biological network. http://www.nimblegen.com/news/events/webinar/podcasts/sebat.m4v Thu, 25 Oct 2007 18:30:00 PDT 00:36:01 autism, CNVs, copy number variation, ROMA, aCGH, comparative genomic hybridization, microarray, genomics, DNA John Rinn, Ph.D., Harvard Medical School Hear the audio of John's presentation on the regulatory role of ncRNAs from the Roche NimbleGen Genetics and Epigenetics Workshop at ASHG, 2007 in San Diego, CA Large Noncoding RNAs (ncRNA) are becoming a distinguishing feature of the Metazoan genomes, but their functional roles are poorly understood. Here we describe a novel type of ncRNA termed HOTAIR that is 2.2. Kb RNA, has 5 spliced exons, a poly A tail and a 5’ meC cap, yet has no potential to code a sensible amino-acid sequence. HOTAIR is encoded antisense to the human HOXC cluster at the exact juncture of a 40 Kb domain of heterochromatin and a 60 Kb domain of euchromatin. However, HOTAIR doesn’t serve to regulate this boundary; Remarkably HOTAIR affects the global epigenetic state of the HOXD cluster located on a separate chromosome. HOTAIR binds the Polycomb Repressive Complex 2 (PRC2) and is required for PRC2 occupancy and histone H3 lysine-27 trimethylation of HOXD locus. Thus, transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance; these results have broad implications for gene regulation in development and disease states. http://www.nimblegen.com/news/events/webinar/podcasts/rinn_ashg.mp3 Thu, 25 Oct 2007 18:30:00 PDT 00:23:09 Tiling expression, ChIP, non-coding, transcription, regulation, NimbleGen, gene expression, microarray, genomics, DNA John Rinn, Ph.D., Harvard Medical School Watch the video of John's presentation on the regulatory role of ncRNAs from the Roche NimbleGen Genetics and Epigenetics Workshop at ASHG, 2007 in San Diego, CA Large Noncoding RNAs (ncRNA) are becoming a distinguishing feature of the Metazoan genomes, but their functional roles are poorly understood. Here we describe a novel type of ncRNA termed HOTAIR that is 2.2. Kb RNA, has 5 spliced exons, a poly A tail and a 5’ meC cap, yet has no potential to code a sensible amino-acid sequence. HOTAIR is encoded antisense to the human HOXC cluster at the exact juncture of a 40 Kb domain of heterochromatin and a 60 Kb domain of euchromatin. However, HOTAIR doesn’t serve to regulate this boundary; Remarkably HOTAIR affects the global epigenetic state of the HOXD cluster located on a separate chromosome. HOTAIR binds the Polycomb Repressive Complex 2 (PRC2) and is required for PRC2 occupancy and histone H3 lysine-27 trimethylation of HOXD locus. Thus, transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance; these results have broad implications for gene regulation in development and disease states. http://www.nimblegen.com/news/events/webinar/podcasts/rinn_ashg.m4v Thu, 25 Oct 2007 18:30:00 PDT 00:23:11 Tiling expression, ChIP, non-coding, transcription, regulation, NimbleGen, gene expression, microarray, genomics, DNA John Rinn, Ph.D., Harvard Medical School Hear the audio portion of John's webinar presentation on the use of NimbleGen ChIP-chip and tiling expression microarrays to explore the role of large non-coding RNAs in the regulation of gene expression. Large Noncoding RNAs (ncRNA) are becoming a distinguishing feature of the Metazoan genomes, but their functional roles are poorly understood. Here we describe a novel type of ncRNA termed HOTAIR that is 2.2. Kb RNA, has 5 spliced exons, a poly A tail and a 5’ meC cap, yet has no potential to code a sensible amino-acid sequence. HOTAIR is encoded antisense to the human HOXC cluster at the exact juncture of a 40 Kb domain of heterochromatin and a 60 Kb domain of euchromatin. However, HOTAIR doesn’t serve to regulate this boundary; Remarkably HOTAIR affects the global epigenetic state of the HOXD cluster located on a separate chromosome. HOTAIR binds the Polycomb Repressive Complex 2 (PRC2) and is required for PRC2 occupancy and histone H3 lysine-27 trimethylation of HOXD locus. Thus, transcription of large ncRNA may demarcate chromosomal domains of gene silencing from a distance. We further discuss RNA labeling optimizations, platform comparisons and the integration of ChIP-Chip and RNA expression on high-resolution DNA tiling arrays that were critical for our discovery of HOTAIR. Together, these results demonstrate the power of integrative genomics in elucidating the biological roles of large ncRNAs. http://www.nimblegen.com/news/events/webinar/podcasts/rinn.mp3 Wed, 19 Sep 2007 11:00:00 CDT 01:05:02 Tiling expression, ChIP, non-coding, Transcription, regulation, NimbleGen, gene expression, microarray, genomics, DNA John Rinn, Ph.D., Harvard Medical School Watch John's webinar presentation on the use of NimbleGen ChIP-chip and tiling expression microarrays to explore the role of large non-coding RNAs in the regulation of gene expression. Large Noncoding RNAs (ncRNA) are becoming a distinguishing feature of the Metazoan genomes, but their functional roles are poorly understood. Here we describe a novel type of ncRNA termed HOTAIR that is 2.2. Kb RNA, has 5 spliced exons, a poly A tail and a 5’ meC cap, yet has no potential to code a sensible amino-acid sequence. HOTAIR is encoded antisense to the human HOXC cluster at the exact juncture of a 40 Kb domain of heterochromatin and a 60 Kb domain of euchromatin. However, HOTAIR doesn’t serve to regulate this boundary; Remarkably HOTAIR affects the global epigenetic state of the HOXD cluster located on a separate chromosome. HOTAIR binds the Polycomb Repressive Complex 2 (PRC2) and is required for PRC2 occupancy and histone H3 lysine-27 trimethylation of HOXD locus. Thus, transcription of large ncRNA may demarcate chromosomal domains of gene silencing from a distance. We further discuss RNA labeling optimizations, platform comparisons and the integration of ChIP-Chip and RNA expression on high-resolution DNA tiling arrays that were critical for our discovery of HOTAIR. Together, these results demonstrate the power of integrative genomics in elucidating the biological roles of large ncRNAs. http://www.nimblegen.com/news/events/webinar/podcasts/rinn.m4v Wed, 19 Sep 2007 11:00:00 CDT 01:04:56 Tiling expression, ChIP, non-coding, Transcription, regulation, NimbleGen, gene expression, microarray, genomics, DNA John Manak, Ph.D., NimbleGen Systems, Inc. Hear the webinar presentation on the reliability and accuracy of NimbleChip Multiplex (4 x 72,000 probes) and one-plex (385,000 probes) for gene expression analysis. Microarray analysis is a powerful tool for quantifying genome-wide changes in gene expression. To facilitate wider application of microarray data in biomedical research and promote the use of microarray analysis in diagnostic and regulatory fields, it is important that data obtained using this technology is accurate and reliable. As such, we evaluated the performance of NimbleGen gene expression microarrays using standard RNA samples recently used by the Microarray Quality Control Consortium, a project established to evaluate the reproducibility and quality of data obtained using microarrays from multiple suppliers. Here we show high inter- array reproducibility was achieved for both the 1-plex and 4-plex expression microarrays, demonstrating the reliability of NimbleChip microarray data. We also show a high concordance between data obtained from NimbleChip microarray analysis and data from TaqMan analysis, the current gold standard for mRNA level quantitation, indicating the accuracy of NimbleChip microarray data in assessing gene expression values. http://www.nimblegen.com/news/events/webinar/podcasts/manak.mp3 Wed, 15 Aug 2007 11:00:00 CDT 00:29:28 MAQC, Taqman, Transcription, regulation, NimbleGen, gene expression, microarray, genomics, DNA John Manak, Ph.D., NimbleGen Systems, Inc. Watch the webinar presentation on the reliability and accuracy of NimbleChip Multiplex (4 x 72,000 probes) and one-plex (385,000 probes) for gene expression analysis. Microarray analysis is a powerful tool for quantifying genome-wide changes in gene expression. To facilitate wider application of microarray data in biomedical research and promote the use of microarray analysis in diagnostic and regulatory fields, it is important that data obtained using this technology is accurate and reliable. As such, we evaluated the performance of NimbleGen gene expression microarrays using standard RNA samples recently used by the Microarray Quality Control Consortium, a project established to evaluate the reproducibility and quality of data obtained using microarrays from multiple suppliers. Here we show high inter- array reproducibility was achieved for both the 1-plex and 4-plex expression microarrays, demonstrating the reliability of NimbleChip microarray data. We also show a high concordance between data obtained from NimbleChip microarray analysis and data from TaqMan analysis, the current gold standard for mRNA level quantitation, indicating the accuracy of NimbleChip microarray data in assessing gene expression values. http://www.nimblegen.com/news/events/webinar/podcasts/manak.m4v Wed, 15 Aug 2007 11:00:00 CDT 00:29:13 MAQC, Taqman, Transcription, regulation, NimbleGen, gene expression, microarray, genomics, DNA Tae Hoon Kim, Ph.D., Yale University School of Medicine Learn about Tae's project analyzing the genome-wide binding sites for the transcriptional repressor CTCF and an analysis of the consensus binding site sequences. Insulator elements affect gene expression by preventing the spread of heterochromatin and restricting transcriptional enhancers from activation of unrelated promoters. In vertebrates, insulator's function requires association with the CCCTC-binding factor (CTCF), a protein that recognizes long and diverse nucleotide sequences. While insulators are critical in gene regulation, only a few have been reported. Here, we describe 13,804 CTCF-binding sites in potential insulators of the human genome, discovered experimentally in primary human fibroblasts. Most of these sequences are located far from the transcriptional start sites, with their distribution strongly correlated with genes. The majority of them fit to a consensus motif highly conserved and suitable for predicting possible insulators driven by CTCF in other vertebrate genomes. In addition, CTCF localization is largely invariant across different cell types. Our results provide a resource for investigating insulator function and possible other general and evolutionarily conserved activities of CTCF sites. http://www.nimblegen.com/news/events/webinar/podcasts/tae.mp3 Wed, 18 Jul 2007 11:00:00 CDT 00:44:55 Repressors, Insulators, Transcription, regulation, NimbleGen, methylation, gene expression, microarray, genomics, DNA Tae Hoon Kim, Ph.D., Yale University School of Medicine Learn about Tae's project analyzing the genome-wide binding sites for the transcriptional repressor CTCF and an analysis of the consensus binding site sequences. Insulator elements affect gene expression by preventing the spread of heterochromatin and restricting transcriptional enhancers from activation of unrelated promoters. In vertebrates, insulator's function requires association with the CCCTC-binding factor (CTCF), a protein that recognizes long and diverse nucleotide sequences. While insulators are critical in gene regulation, only a few have been reported. Here, we describe 13,804 CTCF-binding sites in potential insulators of the human genome, discovered experimentally in primary human fibroblasts. Most of these sequences are located far from the transcriptional start sites, with their distribution strongly correlated with genes. The majority of them fit to a consensus motif highly conserved and suitable for predicting possible insulators driven by CTCF in other vertebrate genomes. In addition, CTCF localization is largely invariant across different cell types. Our results provide a resource for investigating insulator function and possible other general and evolutionarily conserved activities of CTCF sites. http://www.nimblegen.com/news/events/webinar/podcasts/tae.m4v Wed, 18 Jul 2007 11:00:00 CDT 00:44:58 Repressors, Insulators, Transcription, regulation, NimbleGen, methylation, gene expression, microarray, genomics, DNA NimbleGen Systems The full presentation from the NimbleGen Systems Genetics and Epigenetics Workshop at The European Society of Human Genetics Annual Meeting, 2007, Nice, France http://www.nimblegen.com/news/events/webinar/podcasts/eshg2007.mp3 Mon, 18 Jun 2007 07:15:00 CDT 01:16:01 genetics, cancer, NimbleGen, european society of human genetics, CGH, methylation, ChIP-chip, microarray, genomics, DNA NimbleGen Systems The full presentation from the NimbleGen Systems Genetics and Epigenetics Workshop at The European Society of Human Genetics Annual Meeting, 2007, Nice, France http://www.nimblegen.com/news/events/webinar/podcasts/eshg2007.m4v Mon, 18 Jun 2007 07:15:00 CDT 01:16:05 genetics, cancer, NimbleGen, american society of human genetics, CGH, methylation, ChIP-chip, microarray, genomics, DNA Matthew Hurles, Ph.D., The Wellcome Trust Sanger Institute Listen to Matthew's presentation of preliminary data from their project to detect all common CNVs of length 500bp or greater by using NimbleGen array-based CGH on arrays that tile across the assayable portions of the human genome Copy number variation (CNV) in the genome is extensive and yet is grossly under-ascertained. The resolution of CNV detection of most current technology platforms is approximately 50kb, and yet copy number variation two orders of magnitude smaller than this is likely to go undetected by exon resequencing. Furthermore, we know that smaller CNVs are far more numerous than larger CNVs, and so improved CNV detection resolution can be expected to dramatically increase the numbers of known CNVs. We present preliminary data from our project to detect all common CNVs (with minor allele frequencies of 5% of more) of length 500bp or greater by performing array-based comparative genome hybridisation on oligonucleotide arrays that tile across the assayable portions of the human genome. http://www.nimblegen.com/news/events/webinar/podcasts/hurles.mp3 Mon, 18 Jun 2007 07:15:00 CDT 00:22:04 genetics, NimbleGen, copy number variation, CGH, microarray, tiling, DNA Matthew Hurles, Ph.D., The Wellcome Trust Sanger Institute Watch Matthew's presentation of preliminary data from their project to detect all common CNVs of length 500bp or greater by using NimbleGen array-based CGH on arrays that tile across the assayable portions of the human genome Copy number variation (CNV) in the genome is extensive and yet is grossly under-ascertained. The resolution of CNV detection of most current technology platforms is approximately 50kb, and yet copy number variation two orders of magnitude smaller than this is likely to go undetected by exon resequencing. Furthermore, we know that smaller CNVs are far more numerous than larger CNVs, and so improved CNV detection resolution can be expected to dramatically increase the numbers of known CNVs. We present preliminary data from our project to detect all common CNVs (with minor allele frequencies of 5% of more) of length 500bp or greater by performing array-based comparative genome hybridisation on oligonucleotide arrays that tile across the assayable portions of the human genome. http://www.nimblegen.com/news/events/webinar/podcasts/hurles.m4v Mon, 18 Jun 2007 07:15:00 CDT 00:22:05 genetics, NimbleGen, copy number variation, CGH, microarray, tiling, DNA Michal Weber, Ph.D., Friedrich Miescher Institute for Biomedical Research Dr. Weber describes the use of a microarray-based methylation assay, MeDIP, to measure DNA methylation at all human promoters in both somatic cells and gametes DNA methylation at cytosines residues can mediate epigenetic gene silencing and is often perturbed in cancer cells. To gain insight into the function of DNA methylation at promoters and its impact on gene expression, we measure DNA methylation at all human promoters using Methylated DNA Immunoprecipitation (MeDIP) coupled with high density oligonucleotide arrays. We find CpG-poor promoters hypermethylated in somatic cells, which does not preclude their activity. This methylation is present in gametes and results in evolutionary loss of CpG dinucleotides, as measured by divergence between humans and primates. In contrast, strong CpG island promoters are mostly unmethylated, even when inactive. Weak CpG island promoters are distinct, as they are preferential targets for de novo methylation in somatic cells. Notably, most germline-specific genes gain promoter DNA methylation during somatic development, suggesting additional functional selection. These results show that promoter structure and gene function are major predictors of DNA methylation states. http://www.nimblegen.com/news/events/webinar/podcasts/weber.mp3 Mon, 18 Jun 2007 07:15:00 CDT 00:22:51 NimbleGen, MeDIP, methylation, gametes, somatic cells, genomics, DNA, microarray, promoters Michal Weber, Ph.D., Friedrich Miescher Institute for Biomedical Research Dr. Weber describes the use of a microarray-based methylation assay, MeDIP, to measure DNA methylation at all human promoters in both somatic cells and gametes DNA methylation at cytosines residues can mediate epigenetic gene silencing and is often perturbed in cancer cells. To gain insight into the function of DNA methylation at promoters and its impact on gene expression, we measure DNA methylation at all human promoters using Methylated DNA Immunoprecipitation (MeDIP) coupled with high density oligonucleotide arrays. We find CpG-poor promoters hypermethylated in somatic cells, which does not preclude their activity. This methylation is present in gametes and results in evolutionary loss of CpG dinucleotides, as measured by divergence between humans and primates. In contrast, strong CpG island promoters are mostly unmethylated, even when inactive. Weak CpG island promoters are distinct, as they are preferential targets for de novo methylation in somatic cells. Notably, most germline-specific genes gain promoter DNA methylation during somatic development, suggesting additional functional selection. These results show that promoter structure and gene function are major predictors of DNA methylation states. http://www.nimblegen.com/news/events/webinar/podcasts/weber.m4v Mon, 18 Jun 2007 07:15:00 CDT 00:22:51 NimbleGen, MeDIP, methylation, gametes, somatic cells, genomics, DNA, microarray, promoters Joseph Wade In the webinar, Joesph describes work from Kevin Struhl's lab on the genome-wide application of NimbleGen ChIP-chip and tiling gene expression analysis to map both positions of RNA polymerase binding and map transcript locations. A single RNA polymerase is responsible for all transcription in the bacterium Escherichia coli. We have investigated how the genome-wide distribution of this RNA polymerase relates to the level of transcription. Using ChIP-chip we determined the genome-wide association of RNA polymerase. We also determined an unbiased transcript map from the same cells. We identified many novel, non-coding RNAs, including intergenic and intragenic sense and antisense RNAs. Interestingly, there is not a perfect relationship between the distribution of RNA polymerase and the level of transcription. At most transcribed regions RNA polymerase associates with promoters at a much higher level than with coding sequences. Strikingly, almost a quarter of all promoters that bind RNA polymerase are not detectably transcribed. We propose that RNA polymerase is "poised" at these promoters, ready to transcribe the corresponding gene under the appropriate environmental condition. http://www.nimblegen.com/news/events/webinar/podcasts/wade.mp3 Tue, 8 May 2007 11:00:00 CDT 00:45:37 DNA, microarray, RNA, Polymerase, ChIP-chip, gene expression, transcription regulation, promoters Joseph Wade In the webinar, Joesph describes work from Kevin Struhl's lab on the genome-wide application of NimbleGen ChIP-chip and tiling gene expression analysis to map both positions of RNA polymerase binding and map transcript locations. A single RNA polymerase is responsible for all transcription in the bacterium Escherichia coli. We have investigated how the genome-wide distribution of this RNA polymerase relates to the level of transcription. Using ChIP-chip we determined the genome-wide association of RNA polymerase. We also determined an unbiased transcript map from the same cells. We identified many novel, non-coding RNAs, including intergenic and intragenic sense and antisense RNAs. Interestingly, there is not a perfect relationship between the distribution of RNA polymerase and the level of transcription. At most transcribed regions RNA polymerase associates with promoters at a much higher level than with coding sequences. Strikingly, almost a quarter of all promoters that bind RNA polymerase are not detectably transcribed. We propose that RNA polymerase is "poised" at these promoters, ready to transcribe the corresponding gene under the appropriate environmental condition. http://www.nimblegen.com/news/events/webinar/podcasts/wade_webinar.m4v Tue, 8 May 2007 11:00:00 CDT 00:45:42 DNA, microarray, RNA, Polymerase, ChIP-chip, gene expression, transcription regulation, promoters Scott Selleck Part I: In part one, Dr. Selleck will describe the use of fine-tiling array CGH arrays to map chromosomal deletions in human chromosome 10q linked to developmental disorders. We are interested in the genetic underpinnings of behavioral disorders in children. We describe three families with recurrent deletions affecting a region of chromosome 10q that produces a range of language and behavioral deficits. These deletions are in a region with a high density of large low copy repeats (LCRs), suggesting these features of genomic architecture are involved in the production and frequency of these chromosome rearrangements. We have employed NimbleGen oligonucleotide arrays to fine-map these deletions, even those located within LCR elements. Affected genes in this interval include NRG3, GRID1 and PTEN, a tumor suppressor and lipid phosphatase. PTEN mutations have been associated with a subset of autistic children, suggesting signaling regulated by this growth regulator may be involved in autism spectrum disorder. http://www.nimblegen.com/news/events/webinar/podcasts/selleck_part1.mp3 Wed, 11 Apr 2007 11:00:00 CDT 00:32:50 autism, low copy repeats, LCR, array CGH, developmental disorders, axon guidance, drosophila, genetics Scott Selleck Part I: In part one, Dr. Selleck will describe the use of fine-tiling array CGH arrays to map chromosomal deletions in human chromosome 10q linked to developmental disorders. We are interested in the genetic underpinnings of behavioral disorders in children. We describe three families with recurrent deletions affecting a region of chromosome 10q that produces a range of language and behavioral deficits. These deletions are in a region with a high density of large low copy repeats (LCRs), suggesting these features of genomic architecture are involved in the production and frequency of these chromosome rearrangements. We have employed NimbleGen oligonucleotide arrays to fine-map these deletions, even those located within LCR elements. Affected genes in this interval include NRG3, GRID1 and PTEN, a tumor suppressor and lipid phosphatase. PTEN mutations have been associated with a subset of autistic children, suggesting signaling regulated by this growth regulator may be involved in autism spectrum disorder. http://www.nimblegen.com/news/events/webinar/podcasts/selleck_part1.m4v Wed, 11 Apr 2007 11:00:00 CDT 00:32:51 autism, low copy repeats, LCR, array CGH, developmental disorders, axon guidance, drosophila, genetics Scott Selleck Part II: In part two, Dr. Selleck describes the use of Drosophila to model neural growth and development in one of the affected signaling pathways from part one: PTEN (phosphatase and tensin homolog). A second project explores the function of PTEN and other components of this important growth regulatory pathway in neural development, using Drosophila as our model system. We document that the PTEN-TSC-TOR signaling pathway is critical for both axon guidance and synapse assembly. Hyperactivation of this pathway can be genetically or pharmacologically separated from growth effects, yet still produce disruption of neural development, indicating this signaling system has growth-independent roles in neural development. We have also documented behavioral deficits in adult flies with modest activation of this pathway in the nervous system, suggesting Drosophila could provide a useful model for tuberous sclerosis complex. http://www.nimblegen.com/news/events/webinar/podcasts/selleck_part2.mp3 Wed, 11 Apr 2007 11:00:00 CDT 00:33:00 autism, low copy repeats, LCR, array CGH, developmental disorders, axon guidance, drosophila, genetics Scott Selleck Part II: In part two, Dr. Selleck describes the use of Drosophila to model neural growth and development in one of the affected signaling pathways from part one: PTEN (phosphatase and tensin homolog). A second project explores the function of PTEN and other components of this important growth regulatory pathway in neural development, using Drosophila as our model system. We document that the PTEN-TSC-TOR signaling pathway is critical for both axon guidance and synapse assembly. Hyperactivation of this pathway can be genetically or pharmacologically separated from growth effects, yet still produce disruption of neural development, indicating this signaling system has growth-independent roles in neural development. We have also documented behavioral deficits in adult flies with modest activation of this pathway in the nervous system, suggesting Drosophila could provide a useful model for tuberous sclerosis complex. http://www.nimblegen.com/news/events/webinar/podcasts/selleck_part2.m4v Wed, 11 Apr 2007 11:00:00 CDT 00:33:01 autism, low copy repeats, LCR, array CGH, developmental disorders, axon guidance, drosophila, genetics Jason S. Maydan Jason gives a presentation on the application of NimbleGen high-resolution NimbleGen Array CGH to mapping induced and naturally occurring deletions in the genome of C. elegans. We have developed array Comparative Genomic Hybridization for Caenorhabditis elegans as a means of screening for novel induced deletions in this organism. We designed three microarrays consisting of overlapping 50mer probes to annotated exons and micro-RNAs, the first with probes to chromosomes X and II, the second with probes to chromosome II alone, and a third to the entire genome. These arrays were used to reliably detect both a large (50Kb) multigene deletion and a small (1Kb) single-gene deletion in homozygous and heterozygous samples. In one case, a deletion breakpoint was resolved to fewer than 50bp. In an experiment designed to identify new mutations we used the X:II and II arrays to detect deletions associated with lethal mutants on chromosome II. One is an 8Kb deletion targeting the ast-1 gene on chromosome II and another is a 141bp deletion in the gene C06A8.1. Others span large sections of the chromosome, up to 750Kb. As a further application of array Comparative Genomic Hybridization in C. elegans we used the whole-genome array to detect the extensive natural gene content variation (almost 2%) between the N2 Bristol strain and the strain CB4856, a strain isolated in Hawaii and JU258, a strain isolated in Madeira. http://www.nimblegen.com/news/events/webinar/podcasts/maydan_webinar.mp3 Tue, 13 Mar 2007 12:00:00 CDT 00:33:52 genetics, C. elegans, nematode, deletion mutants, NimbleGen, copy number, microarray, genomics, DNA, CGH, comparative genomics hybridization Jason S. Maydan Jason gives a presentation on the application of NimbleGen high-resolution NimbleGen Array CGH to mapping induced and naturally occurring deletions in the genome of C. elegans. We have developed array Comparative Genomic Hybridization for Caenorhabditis elegans as a means of screening for novel induced deletions in this organism. We designed three microarrays consisting of overlapping 50mer probes to annotated exons and micro-RNAs, the first with probes to chromosomes X and II, the second with probes to chromosome II alone, and a third to the entire genome. These arrays were used to reliably detect both a large (50Kb) multigene deletion and a small (1Kb) single-gene deletion in homozygous and heterozygous samples. In one case, a deletion breakpoint was resolved to fewer than 50bp. In an experiment designed to identify new mutations we used the X:II and II arrays to detect deletions associated with lethal mutants on chromosome II. One is an 8Kb deletion targeting the ast-1 gene on chromosome II and another is a 141bp deletion in the gene C06A8.1. Others span large sections of the chromosome, up to >750Kb. As a further application of array Comparative Genomic Hybridization in C. elegans we used the whole-genome array to detect the extensive natural gene content variation (almost 2%) between the N2 Bristol strain and the strain CB4856, a strain isolated in Hawaii and JU258, a strain isolated in Madeira. http://www.nimblegen.com/news/events/webinar/podcasts/maydan_webinar.m4v Tue, 13 Mar 2007 12:00:00 CDT 00:33:56 genetics, C. elegans, nematode, deletion mutants, NimbleGen, copy number, microarray, genomics, DNA, CGH, comparative genomics hybridization Nathaniel Heintzman Nate presents work from the laboratory of Dr. Bing Ren on the application of NimbleGen high-resolution ChIP-chip to the development of predictive algorithms for the identification of novel regulatory elements in the human genome. Eukaryotic gene transcription is accompanied by acetylation and methylation of nucleosomes near promoters, but the locations and roles of histone modifications elsewhere in the genome remain unclear. We determined the chromatin modification states in high resolution along 30 Mb of the human genome and found that active promoters are marked by trimethylation of Lys4 of histone H3 (H3K4), whereas enhancers are marked by monomethylation, but not trimethylation, of H3K4. We developed computational algorithms using these distinct chromatin signatures to identify new regulatory elements, predicting over 200 promoters and 400 enhancers within the 30-Mb region. This approach accurately predicted the location and function of independently identified regulatory elements with high sensitivity and specificity and uncovered a novel functional enhancer for the carnitine transporter SLC22A5 (OCTN2). Our results give insight into the connections between chromatin modifications and transcriptional regulatory activity and provide a new tool for the functional annotation of the human genome. http://www.nimblegen.com/news/events/webinar/podcasts/heintzman.mp3 Tue, 6 Mar 2007 12:00:00 CDT 00:52:57 genetics, histone, enhancers, promoters, gene regulation, NimbleGen, copy number, ChIP-chip, microarray, genomics, DNA Nathaniel Heintzman Nate presents work from the laboratory of Dr. Bing Ren on the application of NimbleGen high-resolution ChIP-chip to the development of predictive algorithms for the identification of novel regulatory elements in the human genome. Eukaryotic gene transcription is accompanied by acetylation and methylation of nucleosomes near promoters, but the locations and roles of histone modifications elsewhere in the genome remain unclear. We determined the chromatin modification states in high resolution along 30 Mb of the human genome and found that active promoters are marked by trimethylation of Lys4 of histone H3 (H3K4), whereas enhancers are marked by monomethylation, but not trimethylation, of H3K4. We developed computational algorithms using these distinct chromatin signatures to identify new regulatory elements, predicting over 200 promoters and 400 enhancers within the 30-Mb region. This approach accurately predicted the location and function of independently identified regulatory elements with high sensitivity and specificity and uncovered a novel functional enhancer for the carnitine transporter SLC22A5 (OCTN2). Our results give insight into the connections between chromatin modifications and transcriptional regulatory activity and provide a new tool for the functional annotation of the human genome. http://www.nimblegen.com/news/events/webinar/podcasts/heintzman.m4v Tue, 6 Mar 2007 12:00:00 CDT 00:53:01 genetics, histone, enhancers, promoters, gene regulation, NimbleGen, copy number, ChIP-chip, microarray, genomics, DNA Timothy A. Graubert, M.D. Tim Graubert, Assistant Professor at Washington University in St. Louis describes his use of NimbleGen Array CGH to identify copy number variation in 21 mouse strains. Submicroscopic (less than 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study 21 well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. We performed comparative genomic hybridization using long oligomer arrays to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies. The CNVs range in size from 21 to 2,002 kb. Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains. Most of the CNVs (77.5%) contain annotated genes, and many (47.5%) colocalize with previously mapped segmental duplications in the mouse genome. We demonstrate that this technique can identify copy number differences associated with known polymorphic traits. The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci. Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits. http://www.nimblegen.com/news/events/webinar/podcasts/graubert.mp3 Thu, 15 Feb 2007 11:00:00 CDT 00:32:13 genetics, research, cancer, NimbleGen, copy number, CNV, Mouse, CGH, comparative genomic hybridization, microarray, genomics, DNA Timothy A. Graubert, M.D. Tim Graubert, Assistant Professor at Washington University in St. Louis describes his use of NimbleGen Array CGH to identify copy number variation in 21 mouse strains. Submicroscopic (less than 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study 21 well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. We performed comparative genomic hybridization using long oligomer arrays to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies. The CNVs range in size from 21 to 2,002 kb. Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains. Most of the CNVs (77.5%) contain annotated genes, and many (47.5%) colocalize with previously mapped segmental duplications in the mouse genome. We demonstrate that this technique can identify copy number differences associated with known polymorphic traits. The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci. Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits. http://www.nimblegen.com/news/events/webinar/podcasts/graubert.m4v Thu, 15 Feb 2007 11:00:00 CDT 00:30:20 genetics, research, cancer, NimbleGen, copy number, CNV, Mouse, CGH, comparative genomic hybridization, microarray, genomics, DNA Daniel Zilberman, Ph.D. Daniel Zilberman describes research using the MeDIP method to analyze DNA methylation in Arabidopsis. http://www.nimblegen.com/news/events/webinar/podcasts/zilberman.mp3 Wed, 24 Jan 2007 11:00:00 CDT 00:45:36 genetics, research, cancer, NimbleGen, immunoprecipitation, methylation, Arabidopsis, ChIP-chip, microarray, genomics, DNA Daniel Zilberman, Ph.D. Daniel Zilberman describes research using the MeDIP method to analyze DNA methylation in Arabidopsis. http://www.nimblegen.com/news/events/webinar/podcasts/zilberman.m4v Wed, 24 Jan 2007 11:00:00 CDT 00:45:36 genetics, research, cancer, NimbleGen, immunoprecipitation, methylation, Arabidopsis, ChIP-chip, microarray, genomics, DNA NimbleGen Systems The full presentation from the NimbleGen Systems Genetics and Epigenetics Workshop at The American Society of Human Genetics Annual Meeting, 2006, New Orleans http://www.nimblegen.com/news/events/webinar/podcasts/ashg_2006.mp3 Tue, 10 Oct 2006 18:30:00 CDT 01:26:07 genetics, cancer, NimbleGen, american society of human genetics, CGH, methylation, ChIP-chip, microarray, genomics, DNA NimbleGen Systems The full presentation from the NimbleGen Systems Genetics and Epigenetics Workshop at The American Society of Human Genetics Annual Meeting, 2006, New Orleans http://www.nimblegen.com/news/events/webinar/podcasts/sashg_2006.m4v Tue, 10 Oct 2006 18:30:00 CDT 01:26:53 genetics, cancer, NimbleGen, american society of human genetics, CGH, methylation, ChIP-chip, microarray, genomics, DNA Andrew Sharp, Ph.D., The University of Washington Andy Sharp presents his latest results using NimbleGen fine-tiling DNA microarrays to map copy-number polymorphisms and the discovery of a previously unreported genomic disease. http://www.nimblegen.com/news/events/webinar/podcasts/sharp_ashg.mp3 Tue, 10 Oct 2006 18:30:00 CDT 00:28:22 genetics, NimbleGen, comparative genome hybridization, CGH, microarray, genomics, DNA Andrew Sharp, Ph.D., The University of Washington Andy Sharp presents his latest results using NimbleGen fine-tiling DNA microarrays to map copy-number polymorphisms and the discovery of a previously unreported genomic disease. http://www.nimblegen.com/news/events/webinar/podcasts/ashg_sharp.m4v Tue, 10 Oct 2006 18:30:00 CDT 00:29:10 genetics, NimbleGen, comparative genome hybridization, CGH, microarray, genomics, DNA John Greally, MD, Ph.D., Albert Einstein College of Medicine John Greally discusses his use of NimbleGen DNA microarrays and his methylation assay, termed the HELP assay, to map DNA methylation patterns associated with cancer genomes http://www.nimblegen.com/news/events/webinar/podcasts/greally_ashg.mp3 Tue, 10 Oct 2006 18:30:00 CDT 00:27:23 genetics, NimbleGen, methylation, epigenetics, microarray, genomics, DNA John Greally, MD, Ph.D., Albert Einstein College of Medicine John Greally discusses his use of NimbleGen DNA microarrays and his methylation assay, termed the HELP assay, to map DNA methylation patterns associated with cancer genomes http://www.nimblegen.com/news/events/webinar/podcasts/ashg_greally.m4v Tue, 10 Oct 2006 18:30:00 CDT 00:27:40 genetics, NimbleGen, methylation, epigenetics, microarray, genomics, DNA Peter Scacheri, Ph.D., Case Western Reserve University Peter Scacheri describes his work using chromatin immunoprecipitation microarray analysis to discover the binding sites of menin, a tumor supressor protein implicated in the human cancer syndrome known as multiple endocrine neoplasia type 1 (MEN1) http://www.nimblegen.com/news/events/webinar/podcasts/scacheri_ashg.mp3 Tue, 10 Oct 2006 18:30:00 CDT 00:21:04 NimbleGen, ChIP-chip, cancer, regulation, microarray, genomics, DNA Peter Scacheri, Ph.D., Case Western Reserve University Peter Scacheri describes his work using chromatin immunoprecipitation microarray analysis to discover the binding sites of menin, a tumor supressor protein implicated in the human cancer syndrome known as multiple endocrine neoplasia type 1 (MEN1) http://www.nimblegen.com/news/events/webinar/podcasts/ashg_scacheri.m4v Tue, 10 Oct 2006 18:30:00 CDT 00:21:22 NimbleGen, ChIP-chip, cancer, regulation, microarray, genomics, DNA Greg Crawford, Ph.D., Duke University Greg Crawford discusses a novel, scalable method for finding DNase I HS sites with NimbleGen microarrays and the implications for scale up to the whole human genome. http://www.nimblegen.com/news/events/webinar/podcasts/crawford.mp3 Tue, 8 Aug 2006 12:00:00 CDT 00:30:20 NimbleGen, comparative genome hybridization, CGH, microarray, genomics, DNA Greg Crawford, Ph.D., Duke University Greg Crawford discusses a novel, scalable method for finding DNase I HS sites with NimbleGen microarrays and the implications for scale up to the whole human genome. http://www.nimblegen.com/news/events/webinar/podcasts/crawford.m4v Tue, 8 Aug 2006 12:00:00 CDT 00:30:20 NimbleGen, DNase, microarray, genomics, DNA Bing Ren, Ph.D., The University of California, San Diego Bing Ren describes his work with chromatin immunoprecipitation microarray analysis (ChIP-chip) to identify regulatory elements throughout the human genome using NimbleGen microarrays http://www.nimblegen.com/news/events/webinar/podcasts/ren_webinar.mp3 Tue, 16 May 2006 12:00:00 CDT 00:33:34 NimbleGen, chromatin, ChIP-chip, microarray, genomics, DNA Bing Ren, Ph.D., The University of California, San Diego Bing Ren describes his work with chromatin immunoprecipitation microarray analysis (ChIP-chip) to identify regulatory elements throughout the human genome using NimbleGen microarrays http://www.nimblegen.com/news/events/webinar/podcasts/ren_webinar.m4v Tue, 16 May 2006 12:00:00 CDT 00:33:34 NimbleGen, chromatin, ChIP-chip, microarray, genomics, DNA yes Douglas Berg, Ph.D., Washington University Doug Berg describes his work finding and characterizing adaptive mutations conferring antibiotic resistance, genome-wide, in the ulcer-causing bacteria Helicobacter pylori using NimbleGen CGS technology http://www.nimblegen.com/news/events/webinar/podcasts/berg_webinar.mp3 Mon, 6 Feb 2006 12:00:00 CST 00:23:01 NimbleGen, mutation, sequencing, antibiotic, microarray, genomics, DNA Douglas Berg, Ph.D., Washington University Doug Berg describes his work finding and characterizing adaptive mutations conferring antibiotic resistance, genome-wide, in the ulcer-causing bacteria Helicobacter pylori using NimbleGen CGS technology http://www.nimblegen.com/news/events/webinar/podcasts/berg_webinar.m4v Mon, 6 Feb 2006 12:00:00 CST 00:23:28 NimbleGen, mutation, sequencing, antibiotic, microarray, genomics, DNA