Search Results - "Eberle, Michael A"

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree by Eberle, Michael A, Fritzilas, Epameinondas, Krusche, Peter, Källberg, Morten, Moore, Benjamin L, Bekritsky, Mitchell A, Iqbal, Zamin, Chuang, Han-Yu, Humphray, Sean J, Halpern, Aaron L, Kruglyak, Semyon, Margulies, Elliott H, McVean, Gil, Bentley, David R

“…Improvement of variant calling in next-generation sequence data requires a comprehensive, genome-wide catalog of high-confidence variants called in a set of…”
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Paragraph: a graph-based structural variant genotyper for short-read sequence data by Chen, Sai, Krusche, Peter, Dolzhenko, Egor, Sherman, Rachel M, Petrovski, Roman, Schlesinger, Felix, Kirsche, Melanie, Bentley, David R, Schatz, Michael C, Sedlazeck, Fritz J, Eberle, Michael A

“…Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical…”
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ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions by Dolzhenko, Egor, Deshpande, Viraj, Schlesinger, Felix, Krusche, Peter, Petrovski, Roman, Chen, Sai, Emig-Agius, Dorothea, Gross, Andrew, Narzisi, Giuseppe, Bowman, Brett, Scheffler, Konrad, van Vugt, Joke J F A, French, Courtney, Sanchis-Juan, Alba, Ibáñez, Kristina, Tucci, Arianna, Lajoie, Bryan R, Veldink, Jan H, Raymond, F Lucy, Taft, Ryan J, Bentley, David R, Eberle, Michael A

“…Abstract Summary We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to…”
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Repeat expansions confer WRN dependence in microsatellite-unstable cancers by van Wietmarschen, Niek, Sridharan, Sriram, Nathan, William J., Tubbs, Anthony, Chan, Edmond M., Callen, Elsa, Wu, Wei, Belinky, Frida, Tripathi, Veenu, Wong, Nancy, Foster, Kyla, Noorbakhsh, Javad, Garimella, Kiran, Cruz-Migoni, Abimael, Sommers, Joshua A., Huang, Yongqing, Borah, Ashir A., Smith, Jonathan T., Kalfon, Jeremie, Kesten, Nikolas, Fugger, Kasper, Walker, Robert L., Dolzhenko, Egor, Eberle, Michael A., Hayward, Bruce E., Usdin, Karen, Freudenreich, Catherine H., Brosh, Robert M., West, Stephen C., McHugh, Peter J., Meltzer, Paul S., Bass, Adam J., Nussenzweig, André

“…The RecQ DNA helicase WRN is a synthetic lethal target for cancer cells with microsatellite instability (MSI), a form of genetic hypermutability that arises…”
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Bioinformatics-Based Identification of Expanded Repeats: A Non-reference Intronic Pentamer Expansion in RFC1 Causes CANVAS by Rafehi, Haloom, Szmulewicz, David J., Bennett, Mark F., Sobreira, Nara L.M., Pope, Kate, Smith, Katherine R., Gillies, Greta, Diakumis, Peter, Dolzhenko, Egor, Eberle, Michael A., Barcina, María García, Breen, David P., Chancellor, Andrew M., Cremer, Phillip D., Delatycki, Martin B., Fogel, Brent L., Hackett, Anna, Halmagyi, G. Michael, Kapetanovic, Solange, Lang, Anthony, Mossman, Stuart, Mu, Weiyi, Patrikios, Peter, Perlman, Susan L., Rosemergy, Ian, Storey, Elsdon, Watson, Shaun R.D., Wilson, Michael A., Zee, David S., Valle, David, Amor, David J., Bahlo, Melanie, Lockhart, Paul J.

“…Genomic technologies such as next-generation sequencing (NGS) are revolutionizing molecular diagnostics and clinical medicine. However, these approaches have…”
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Length of Uninterrupted CAG, Independent of Polyglutamine Size, Results in Increased Somatic Instability, Hastening Onset of Huntington Disease by Wright, Galen E.B., Collins, Jennifer A., Kay, Chris, McDonald, Cassandra, Dolzhenko, Egor, Xia, Qingwen, Bečanović, Kristina, Drögemöller, Britt I., Semaka, Alicia, Nguyen, Charlotte M., Trost, Brett, Richards, Fiona, Bijlsma, Emilia K., Squitieri, Ferdinando, Ross, Colin J.D., Scherer, Stephen W., Eberle, Michael A., Yuen, Ryan K.C., Hayden, Michael R.

“…Huntington disease (HD) is caused by a CAG repeat expansion in the huntingtin (HTT) gene. Although the length of this repeat is inversely correlated with age…”
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ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data by Dolzhenko, Egor, Bennett, Mark F, Richmond, Phillip A, Trost, Brett, Chen, Sai, van Vugt, Joke J F A, Nguyen, Charlotte, Narzisi, Giuseppe, Gainullin, Vladimir G, Gross, Andrew M, Lajoie, Bryan R, Taft, Ryan J, Wasserman, Wyeth W, Scherer, Stephen W, Veldink, Jan H, Bentley, David R, Yuen, Ryan K C, Bahlo, Melanie, Eberle, Michael A

“…Repeat expansions are responsible for over 40 monogenic disorders, and undoubtedly more pathogenic repeat expansions remain to be discovered. Existing methods…”
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Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions by Rajan-Babu, Indhu-Shree, Peng, Junran J, Chiu, Readman, Li, Chenkai, Mohajeri, Arezoo, Dolzhenko, Egor, Eberle, Michael A, Birol, Inanc, Friedman, Jan M

“…Screening for short tandem repeat (STR) expansions in next-generation sequencing data can enable diagnosis, optimal clinical management/treatment, and accurate…”
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Mapping complex disease loci in whole-genome association studies by Carlson, Christopher S, Eberle, Michael A, Kruglyak, Leonid, Nickerson, Deborah A

“…Identification of the genetic polymorphisms that contribute to susceptibility for common diseases such as type 2 diabetes and schizophrenia will aid in the…”
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Whole-genome haplotyping by dilution, amplification, and sequencing by Kaper, Fiona, Swamy, Sajani, Klotzle, Brandy, Munchel, Sarah, Cottrell, Joseph, Bibikova, Marina, Chuang, Han-Yu, Kruglyak, Semyon, Ronaghi, Mostafa, Eberle, Michael A., Fan, Jian-Bing

“…Standard whole-genome genotyping technologies are unable to determine haplotypes. Here we describe a method for rapid and cost-effective long-range…”
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REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats by Dolzhenko, Egor, Weisburd, Ben, Ibañez, Kristina, Rajan-Babu, Indhu-Shree, Anyansi, Christine, Bennett, Mark F, Billingsley, Kimberley, Carroll, Ashley, Clamons, Samuel, Danzi, Matt C, Deshpande, Viraj, Ding, Jinhui, Fazal, Sarah, Halman, Andreas, Jadhav, Bharati, Qiu, Yunjiang, Richmond, Phillip A, Saunders, Christopher T, Scheffler, Konrad, van Vugt, Joke J F A, Zwamborn, Ramona R A J, Chong, Samuel S, Friedman, Jan M, Tucci, Arianna, Rehm, Heidi L, Eberle, Michael A

“…Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many…”
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Population history and natural selection shape patterns of genetic variation in 132 genes by Akey, Joshua M, Eberle, Michael A, Rieder, Mark J, Carlson, Christopher S, Shriver, Mark D, Nickerson, Deborah A, Kruglyak, Leonid

“…Identifying regions of the human genome that have been targets of natural selection will provide important insights into human evolutionary history and may…”
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Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk by Behera, Sairam, Belyeu, Jonathan R, Chen, Xiao, Paulin, Luis F, Nguyen, Ngoc Quynh H, Newman, Emma, Mahmoud, Medhat, Menon, Vipin K, Qi, Qibin, Joshi, Parag, Marcovina, Santica, Rossi, Massimiliano, Roller, Eric, Han, James, Onuchic, Vitor, Avery, Christy L, Ballantyne, Christie M, Rodriguez, Carlos J, Kaplan, Robert C, Muzny, Donna M, Metcalf, Ginger A, Gibbs, Richard A, Yu, Bing, Boerwinkle, Eric, Eberle, Michael A, Sedlazeck, Fritz J

“…The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN)…”
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Genomic regions exhibiting positive selection identified from dense genotype data by Carlson, Christopher S, Thomas, Daryl J, Eberle, Michael A, Swanson, Johanna E, Livingston, Robert J, Rieder, Mark J, Nickerson, Deborah A

“…The allele frequency spectrum of polymorphisms in DNA sequences can be used to test for signatures of natural selection that depart from the expected frequency…”
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Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson’s disease-associated GBA gene by Toffoli, Marco, Chen, Xiao, Sedlazeck, Fritz J., Lee, Chiao-Yin, Mullin, Stephen, Higgins, Abigail, Koletsi, Sofia, Garcia-Segura, Monica Emili, Sammler, Esther, Scholz, Sonja W., Schapira, Anthony H. V., Eberle, Michael A., Proukakis, Christos

“…GBA variants carriers are at increased risk of Parkinson’s disease (PD) and Lewy body dementia (LBD). The presence of pseudogene GBAP1 predisposes to…”
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Extensive and breed-specific linkage disequilibrium in Canis familiaris by Sutter, Nathan B, Eberle, Michael A, Parker, Heidi G, Pullar, Barbara J, Kirkness, Ewen F, Kruglyak, Leonid, Ostrander, Elaine A

“…The 156 breeds of registered dogs in the United States offer a unique opportunity to map genes important in disease susceptibility, morphology, and behavior…”
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Correction to: Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions by Rajan-Babu, Indhu-Shree, Peng, Junran J, Chiu, Readman, Li, Chenkai, Mohajeri, Arezoo, Dolzhenko, Egor, Eberle, Michael A, Birol, Inanc, Friedman, Jan M

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Power to detect risk alleles using genome-wide tag SNP panels by Eberle, Michael A, Ng, Pauline C, Kuhn, Kenneth, Zhou, Lixin, Peiffer, Daniel A, Galver, Luana, Viaud-Martinez, Karine A, Lawley, Cynthia Taylor, Gunderson, Kevin L, Shen, Richard, Murray, Sarah S

“…Advances in high-throughput genotyping and the International HapMap Project have enabled association studies at the whole-genome level. We have constructed…”
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Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome by Eberle, Michael A, Rieder, Mark J, Kruglyak, Leonid, Nickerson, Deborah A

“…Significant interest has emerged in mapping genetic susceptibility for complex traits through whole-genome association studies. These studies rely on the…”
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Comprehensive SMN1 and SMN2 profiling for spinal muscular atrophy analysis using long-read PacBio HiFi sequencing by Chen, Xiao, Harting, John, Farrow, Emily, Thiffault, Isabelle, Kasperaviciute, Dalia, Hoischen, Alexander, Gilissen, Christian, Pastinen, Tomi, Eberle, Michael A.

“…Spinal muscular atrophy, a leading cause of early infant death, is caused by bi-allelic mutations of SMN1. Sequence analysis of SMN1 is challenging due to high…”
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