The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Konrad J Karczewski - One of the best experts on this subject based on the ideXlab platform.
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the exac browser displaying reference data information from over 60 000 Exomes
Nucleic Acids Research, 2017Co-Authors: Konrad J Karczewski, Ben Weisburd, Brett Thomas, Douglas M Ruderfer, David H Kavanagh, Matthew Solomonson, Tymor HamamsyAbstract:Worldwide, hundreds of thousands of humans have had their genomes or Exomes sequenced, and access to the resulting data sets can provide valuable information for variant interpretation and understanding gene function. Here, we present a lightweight, flexible browser framework to display large population datasets of genetic variation. We demonstrate its use for Exome sequence data from 60 706 individuals in the Exome Aggregation Consortium (ExAC). The ExAC browser provides gene- and transcript-centric displays of variation, a critical view for clinical applications. Additionally, we provide a variant display, which includes population frequency and functional annotation data as well as short read support for the called variant. This browser is open-source, freely available at http://exac.broadinstitute.org, and has already been used extensively by clinical laboratories worldwide.
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the exac browser displaying reference data information from over 60 000 Exomes
bioRxiv, 2016Co-Authors: Konrad J Karczewski, Ben Weisburd, Brett Thomas, Douglas M Ruderfer, David H Kavanagh, Tymor Hamamsy, Monkol Lek, Kaitlin E Samocha, Beryl B Cummings, Daniel P BirnbaumAbstract:Worldwide, hundreds of thousands of humans have had their genomes or Exomes sequenced, and access to the resulting data sets can provide valuable information for variant interpretation and understanding gene function. Here, we present a lightweight, flexible browser framework to display large population datasets of genetic variation. We demonstrate its use for Exome sequence data from 60,706 individuals in the Exome Aggregation Consortium (ExAC). The ExAC browser provides gene- and transcript-centric displays of variation, a critical view for clinical applications. Additionally, we provide a variant display, which includes population frequency and functional annotation data as well as short read support for the called variant. This browser is open-source, freely available, and has already been used extensively by clinical laboratories worldwide.
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performance comparison of Exome dna sequencing technologies
Nature Biotechnology, 2011Co-Authors: Michael J Clark, Konrad J Karczewski, Rui Chen, Hugo Y K Lam, Rong Chen, Ghia Euskirchen, Atul J Butte, Michael SnyderAbstract:Whole Exome sequencing by high-throughput sequencing of target-enriched genomic DNA (Exome-seq) has become common in basic and translational research as a means of interrogating the interpretable part of the human genome at relatively low cost. We present a comparison of three major commercial Exome sequencing platforms from Agilent, Illumina and Nimblegen applied to the same human blood sample. Our results suggest that the Nimblegen platform, which is the only one to use high-density overlapping baits, covers fewer genomic regions than the other platforms but requires the least amount of sequencing to sensitively detect small variants. Agilent and Illumina are able to detect a greater total number of variants with additional sequencing. Illumina captures untranslated regions, which are not targeted by the Nimblegen and Agilent platforms. We also compare Exome sequencing and whole genome sequencing (WGS) of the same sample, demonstrating that Exome sequencing can detect additional small variants missed by WGS.
David A. Mackey - One of the best experts on this subject based on the ideXlab platform.
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Contribution of mutations in known Mendelian glaucoma genes to advanced early-onset primary open-angle glaucoma
Investigative Ophthalmology & Visual Science, 2017Co-Authors: Tiger Zhou, John Landers, Emmanuelle Souzeau, Alex W Hewitt, Richard Mills, Paul R Healey, Ivan Goldberg, Owen M Siggs, Stuart L Graham, David A. MackeyAbstract:PURPOSE. Primary open-angle glaucoma (POAG) and primary congenital glaucoma (PCG) with Mendelian inheritance are caused by mutations in at least nine genes. Utilizing whole-Exome sequencing, we examined the disease burden accounted for by these known Mendelian glaucoma genes in a cohort of individuals with advanced early-onset POAG. METHODS. The cases exhibited advanced POAG with young age of diagnosis. Cases and examined local controls were subjected to whole-Exome sequencing. Nine hundred ninetythree previously sequenced Exomes of Australian controls were called jointly with our dataset. Qualifying variants were selected based on predicted pathogenicity and rarity in public domain gene variant databases. Case-control mutational burdens were calculated for glaucoma-linked genes. RESULTS. Two hundred eighteen unrelated POAG participants and 103 nonglaucomatous controls were included in addition to 993 unexamined controls. Fifty-eight participants (26.6%) harbored rare potentially pathogenic variants in known glaucoma genes. Enrichment of qualifying variants toward glaucoma was present in all genes except WDR36, in which controls harbored more variants, and TBK1, in which no qualifying variants were detected in cases or controls. After multiple testing correction, only MYOC showed statistically significant enrichment of qualifying variants (odds ratio [OR] = 16.62, P = 6.31310). CONCLUSIONS. Rare, potentially disease-causing variants in Mendelian POAG genes that showed enrichment in our dataset were found in 22.9% of advanced early-onset POAG cases. MYOC variants represented the largest monogenic cause in POAG. The association between WDR36 and POAG was not supported, and the majority of POAG cases did not harbor a potentially disease-causing variant in the remaining Mendelian genes.
Tymor Hamamsy - One of the best experts on this subject based on the ideXlab platform.
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the exac browser displaying reference data information from over 60 000 Exomes
Nucleic Acids Research, 2017Co-Authors: Konrad J Karczewski, Ben Weisburd, Brett Thomas, Douglas M Ruderfer, David H Kavanagh, Matthew Solomonson, Tymor HamamsyAbstract:Worldwide, hundreds of thousands of humans have had their genomes or Exomes sequenced, and access to the resulting data sets can provide valuable information for variant interpretation and understanding gene function. Here, we present a lightweight, flexible browser framework to display large population datasets of genetic variation. We demonstrate its use for Exome sequence data from 60 706 individuals in the Exome Aggregation Consortium (ExAC). The ExAC browser provides gene- and transcript-centric displays of variation, a critical view for clinical applications. Additionally, we provide a variant display, which includes population frequency and functional annotation data as well as short read support for the called variant. This browser is open-source, freely available at http://exac.broadinstitute.org, and has already been used extensively by clinical laboratories worldwide.
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the exac browser displaying reference data information from over 60 000 Exomes
bioRxiv, 2016Co-Authors: Konrad J Karczewski, Ben Weisburd, Brett Thomas, Douglas M Ruderfer, David H Kavanagh, Tymor Hamamsy, Monkol Lek, Kaitlin E Samocha, Beryl B Cummings, Daniel P BirnbaumAbstract:Worldwide, hundreds of thousands of humans have had their genomes or Exomes sequenced, and access to the resulting data sets can provide valuable information for variant interpretation and understanding gene function. Here, we present a lightweight, flexible browser framework to display large population datasets of genetic variation. We demonstrate its use for Exome sequence data from 60,706 individuals in the Exome Aggregation Consortium (ExAC). The ExAC browser provides gene- and transcript-centric displays of variation, a critical view for clinical applications. Additionally, we provide a variant display, which includes population frequency and functional annotation data as well as short read support for the called variant. This browser is open-source, freely available, and has already been used extensively by clinical laboratories worldwide.
Ben Weisburd - One of the best experts on this subject based on the ideXlab platform.
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the exac browser displaying reference data information from over 60 000 Exomes
Nucleic Acids Research, 2017Co-Authors: Konrad J Karczewski, Ben Weisburd, Brett Thomas, Douglas M Ruderfer, David H Kavanagh, Matthew Solomonson, Tymor HamamsyAbstract:Worldwide, hundreds of thousands of humans have had their genomes or Exomes sequenced, and access to the resulting data sets can provide valuable information for variant interpretation and understanding gene function. Here, we present a lightweight, flexible browser framework to display large population datasets of genetic variation. We demonstrate its use for Exome sequence data from 60 706 individuals in the Exome Aggregation Consortium (ExAC). The ExAC browser provides gene- and transcript-centric displays of variation, a critical view for clinical applications. Additionally, we provide a variant display, which includes population frequency and functional annotation data as well as short read support for the called variant. This browser is open-source, freely available at http://exac.broadinstitute.org, and has already been used extensively by clinical laboratories worldwide.
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the exac browser displaying reference data information from over 60 000 Exomes
bioRxiv, 2016Co-Authors: Konrad J Karczewski, Ben Weisburd, Brett Thomas, Douglas M Ruderfer, David H Kavanagh, Tymor Hamamsy, Monkol Lek, Kaitlin E Samocha, Beryl B Cummings, Daniel P BirnbaumAbstract:Worldwide, hundreds of thousands of humans have had their genomes or Exomes sequenced, and access to the resulting data sets can provide valuable information for variant interpretation and understanding gene function. Here, we present a lightweight, flexible browser framework to display large population datasets of genetic variation. We demonstrate its use for Exome sequence data from 60,706 individuals in the Exome Aggregation Consortium (ExAC). The ExAC browser provides gene- and transcript-centric displays of variation, a critical view for clinical applications. Additionally, we provide a variant display, which includes population frequency and functional annotation data as well as short read support for the called variant. This browser is open-source, freely available, and has already been used extensively by clinical laboratories worldwide.
Brett Thomas - One of the best experts on this subject based on the ideXlab platform.
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the exac browser displaying reference data information from over 60 000 Exomes
Nucleic Acids Research, 2017Co-Authors: Konrad J Karczewski, Ben Weisburd, Brett Thomas, Douglas M Ruderfer, David H Kavanagh, Matthew Solomonson, Tymor HamamsyAbstract:Worldwide, hundreds of thousands of humans have had their genomes or Exomes sequenced, and access to the resulting data sets can provide valuable information for variant interpretation and understanding gene function. Here, we present a lightweight, flexible browser framework to display large population datasets of genetic variation. We demonstrate its use for Exome sequence data from 60 706 individuals in the Exome Aggregation Consortium (ExAC). The ExAC browser provides gene- and transcript-centric displays of variation, a critical view for clinical applications. Additionally, we provide a variant display, which includes population frequency and functional annotation data as well as short read support for the called variant. This browser is open-source, freely available at http://exac.broadinstitute.org, and has already been used extensively by clinical laboratories worldwide.
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the exac browser displaying reference data information from over 60 000 Exomes
bioRxiv, 2016Co-Authors: Konrad J Karczewski, Ben Weisburd, Brett Thomas, Douglas M Ruderfer, David H Kavanagh, Tymor Hamamsy, Monkol Lek, Kaitlin E Samocha, Beryl B Cummings, Daniel P BirnbaumAbstract:Worldwide, hundreds of thousands of humans have had their genomes or Exomes sequenced, and access to the resulting data sets can provide valuable information for variant interpretation and understanding gene function. Here, we present a lightweight, flexible browser framework to display large population datasets of genetic variation. We demonstrate its use for Exome sequence data from 60,706 individuals in the Exome Aggregation Consortium (ExAC). The ExAC browser provides gene- and transcript-centric displays of variation, a critical view for clinical applications. Additionally, we provide a variant display, which includes population frequency and functional annotation data as well as short read support for the called variant. This browser is open-source, freely available, and has already been used extensively by clinical laboratories worldwide.
