http://www.nimblegen.com/news/events/webinar/index.html en-us 2009 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 A. Leonardo Iniguez Hear Leo's presentation on the NimbleGen 2.1M DNA Methylation Arrays. http://test.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://test.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 Jamel Chelly Hear Jamel's presentation on genomic copy number variant analysis from the Roche NimbleGen workshop at the ESHG 2008 Annual Meeting in Barcelona, Spain. http://www.nimblegen.com/news/events/webinar/podcasts/chelly_eshg.mp3 Mon, 2 Jun 2008 20:00:00 CDT 00:25:55 NimbleGen, CGH, microarray, copy-number variants, CNV, Barcelona, ESHG, Roche Jamel Chelly Watch Jamel's presentation on genomic copy number variant analysis from the Roche NimbleGen workshop at the ESHG 2008 Annual Meeting in Barcelona, Spain. http://www.nimblegen.com/news/events/webinar/podcasts/chelly.m4v Mon, 2 Jun 2008 20:00:00 CDT 00:25:55 NimbleGen, CGH, microarray, copy-number variants, CNV, Barcelona, ESHG, Roche 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 Roche NimbleGen Hear the entire program from the ASHG 2007 Roche NimbleGen Genetics and Epigenetics Workshop Human Genetics and Epigenetics: High-Definition Analysis of: DNA Copy Number Variation in Autism, Application of CGH Arrays in Clinical Diagnostics and Expression Regulation by Non-Coding RNAs http://www.nimblegen.com/news/events/webinar/podcasts/ashg_2007.mp3 Thu, 25 Oct 2007 18:30:00 PDT 1:23:00 autism, HOX, microarray, diagnostics, aCGH, comparative genomic hybridization, CGH, RETT syndrome, polyposis, cystic fibrosis, muscular dystrophy, NSD1, DNA Roche NimbleGen Watch the entire program from the ASHG 2007 Roche NimbleGen Genetics and Epigenetics Workshop Human Genetics and Epigenetics: High-Definition Analysis of: DNA Copy Number Variation in Autism, Application of CGH Arrays in Clinical Diagnostics and Expression Regulation by Non-Coding RNAs http://www.nimblegen.com/news/events/webinar/podcasts/ashg_2007.m4v Thu, 25 Oct 2007 18:30:00 PDT 1:26:51 autism, HOX, microarray, diagnostics, aCGH, comparative genomic hybridization, CGH, RETT syndrome, polyposis, cystic fibrosis, muscular dystrophy, NSD1, DNA 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 Dr. Madhuri Hegde, Emory University School of Medicine Hear Madhuri's presentation on the diagnostic application of NimbleGen Array CGH from the Roche NimbleGen Genetics and Epigenetics Workshop at ASHG, 2007 in San Diego, CA Molecular methods used in DNA diagnostic laboratories to detect single exon or large deletions and duplications in a single gene involve multiplex PCR amplification, quantitative PCR, Southern blotting, MLPA, DOVAM-S and SCAIP. These methods are time consuming, laborious and do not accurately detect all mutations. We have developed a high resolution approach using CGH arrays to comprehensively detect single exon or large deletions and duplications mutations. One of the biggest challenges in genetic testing is evaluation of analytical and clinical validity for each genetic test. We describe here for the first time the development, design and validation of CGH arrays for detecting single exon or large deletions and duplications in autosomal and X-linked disease associated genes in a DNA diagnostic laboratory. The CGH arrays can be easily adopted in the clinical molecular testing laboratories and is a rapid and very cost effective approach to screen single exon or large deletions and duplications. http://www.nimblegen.com/news/events/webinar/podcasts/hegde.mp3 Thu, 25 Oct 2007 18:30:00 PDT 00:23:51 diagnostics, aCGH, comparative genomic hybridization, CGH, RETT syndrome, polyposis, cystic fibrosis, muscular dystrophy, NSD1, DNA Dr. Madhuri Hegde, Emory University School of Medicine Watch Madhuri's presentation on the diagnostic application of NimbleGen Array CGH from the Roche NimbleGen Genetics and Epigenetics Workshop at ASHG, 2007 in San Diego, CA Molecular methods used in DNA diagnostic laboratories to detect single exon or large deletions and duplications in a single gene involve multiplex PCR amplification, quantitative PCR, Southern blotting, MLPA, DOVAM-S and SCAIP. These methods are time consuming, laborious and do not accurately detect all mutations. We have developed a high resolution approach using CGH arrays to comprehensively detect single exon or large deletions and duplications mutations. One of the biggest challenges in genetic testing is evaluation of analytical and clinical validity for each genetic test. We describe here for the first time the development, design and validation of CGH arrays for detecting single exon or large deletions and duplications in autosomal and X-linked disease associated genes in a DNA diagnostic laboratory. The CGH arrays can be easily adopted in the clinical molecular testing laboratories and is a rapid and very cost effective approach to screen single exon or large deletions and duplications. http://www.nimblegen.com/news/events/webinar/podcasts/hegde.m4v Thu, 25 Oct 2007 18:30:00 PDT 00:23:53 diagnostics, aCGH, comparative genomic hybridization, CGH, RETT syndrome, polyposis, cystic fibrosis, muscular dystrophy, NSD1, 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 Gerd Pfeifer In the webinar, Gerd describes the alterations of DNA methylation patterns in tumor samples using 'MIRA', the methylated CpG island recovery assay in conjunction with microarray analysis to map DNA methylation patterns across entire cancer genomes. Alterations in DNA methylation patterns occur in every type of human cancer and are considered a hallmark of malignant transformation. Most notable is the cancer-associated hypermethylation of CpG-rich sequences, the so-called CpG islands, which are often found near the 5 ends and promoters of genes. This CpG island methylation represents a positive signal that can be used to distinguish malignant tissue from normal tissue. Thus, characterization of CpG island hypermethylation has become a valuable tool for cancer detection and diagnosis. Besides looking at individual genes, an even greater potential lies in the characterization of genome-wide changes of DNA methylation patterns in tumors. It is likely that tumor-type and tumor-subtype-specific DNA methylation patterns exist and can be exploited for the classification of cancers, their response to therapy and their metastatic potential, and thus may have predictive value. Various methods for genome-wide analysis of DNA methylation have been developed. In this presentation, we will focus on the methylated-CpG island recovery assay (MIRA), which has been used in combination with microarray analysis to map CpG island methylation across cancer genomes. http://www.nimblegen.com/news/events/webinar/podcasts/pfeifer.mp3 Thu, 17 May 2007 12:00:00 CDT 00:53:46 DNA, microarray, CpG, Methylation, MIRA, MeDIP, epigenomics, promoters Gerd Pfeifer In the webinar, Gerd describes the alterations of DNA methylation patterns in tumor samples using 'MIRA', the methylated CpG island recovery assay in conjunction with microarray analysis to map DNA methylation patterns across entire cancer genomes. Alterations in DNA methylation patterns occur in every type of human cancer and are considered a hallmark of malignant transformation. Most notable is the cancer-associated hypermethylation of CpG-rich sequences, the so-called CpG islands, which are often found near the 5 ends and promoters of genes. This CpG island methylation represents a positive signal that can be used to distinguish malignant tissue from normal tissue. Thus, characterization of CpG island hypermethylation has become a valuable tool for cancer detection and diagnosis. Besides looking at individual genes, an even greater potential lies in the characterization of genome-wide changes of DNA methylation patterns in tumors. It is likely that tumor-type and tumor-subtype-specific DNA methylation patterns exist and can be exploited for the classification of cancers, their response to therapy and their metastatic potential, and thus may have predictive value. Various methods for genome-wide analysis of DNA methylation have been developed. In this presentation, we will focus on the methylated-CpG island recovery assay (MIRA), which has been used in combination with microarray analysis to map CpG island methylation across cancer genomes. http://www.nimblegen.com/news/events/webinar/podcasts/pfeifer_webinar.m4v Thu, 17 May 2007 12:00:00 CDT 00:53:49 DNA, microarray, CpG, Methylation, MIRA, MeDIP, epigenomics, 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 Blake Ballif This is the audio of a presentation by Blake Ballif of Signature Genomic Laboratories at the NimbleGen workshop at ACMG 2007 in Nashville, TN, on the use of NimbleGen Array CGH to analyze very small genomic amplifications and deletions. This is the audio of a presentation by Blake Ballif of Signature Genomic Laboratories at the NimbleGen workshop at ACMG 2007 in Nashville, TN, on the use of NimbleGen Array CGH to analyze very small genomic amplifications and deletions. http://www.nimblegen.com/news/events/webinar/podcasts/ballif.mp3 Sat, 24 Mar 2007 12:00:00 CDT 00:25:40 genetics, deletion mutants, NimbleGen, copy number, microarray, genomics, DNA, CGH, comparative genomics hybridization Blake Ballif This is the video and audio of a presentation by Blake Ballif of Signature Genomic Laboratories at the NimbleGen workshop at ACMG 2007 in Nashville, TN, on the use of NimbleGen Array CGH to analyze very small genomic amplifications and deletions. This is the video and audio of a presentation by Blake Ballif of Signature Genomic Laboratories at the NimbleGen workshop at ACMG 2007 in Nashville, TN, on the use of NimbleGen Array CGH to analyze very small genomic amplifications and deletions. http://www.nimblegen.com/news/events/webinar/podcasts/ballif.m4v Sat, 24 Mar 2007 12:00:00 CDT 00:25:41 genetics, 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.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