ASHG 2012: Human Genetics Becomes “Next-Generation Human Genomics”

ASHG2012: Human genetics becomes "Next-Gen Human Genomics"

ASHG2012: Human genetics becomes “Next-Gen Human Genomics”

American Society of Human Genetics (ASHG)’s 62nd Annual Meeting is kicking off in a week (Tuesday, November 6 ) in San Francisco, CA, at the Moscone Center.  The five day conference covers the latest on all aspects of human genetics research. Among many interesting things to look for at the conference (like the Illumina MiSeq winners), one is the role of next-gen sequencing in human genetics research.

If you have any doubt, human genetics has turned into “Next Generation Human Genomics” with next-gen sequencing, just a quick look at the abstract/program schedule shows that majority of the work to be presented involve next-generation sequencing, be it exome sequencing or whole genome sequencing or RNA-Seq.

A search at the this year’s abstracts book (pdf file of platform abstracts) for the word “exome” shows that “exome” is mentioned “293” times (more than 500 times if one includes posters).  The word “exome” is mentioned in the title/abstract only 153 times in last year ASHG’s platform abstracts.  The whopping close to “100%” increase in “exome” clearly shows the impact of next generation sequencing on human genetics. Next-gen human genetics is for here to stay and pretty soon we’ll get over the “OMG NGS” syndrome.

Here is the “almost” complete list of platform presentations that has the word “exome” in the title at the ASHG meeting this year. Visit ASHG 2012 for all things next-generation human genetics.

ASHG 2012: Tuesday, November 6

 Lessons Learned from the NHLBI-Exome Sequencing Project. S. M. Leal on behalf of the NHLBI-Exome Sequencing Project Molec/Human Gen, Baylor Col Med, Houston, TX.

ASHG 2012: Wednesday, November 7

Identifying inherited autism mutations using whole exome sequencing. T. W. Yu, M. H. Chahrour, M. E. Coulter, S. Jiralerspong, K. Okamura-Ikeda, K. Schmitz-Abe, G. H. Mochida, J. N. Partlow, R. S. Hill, M. Al-Saffar, N. M. Mukaddes, A. Hashmi, S. Balkhy, G. G. Gascon, O. Oner, S. Al-Saad, T. Ben-Omran, L. Al-Gazali, V. Eapen, C. Stevens, S. Gabriel, K. Markianos, H. Taniguchi, N. E. Braverman, E. M. Morrow, C. A. Walsh.

Identical by descent filtering in extended families reveals novel autism genes detected by exome sequencing. H. N. Cukier, N. D. Dueker, S. H. Slifer, J. M. Lee, P. L. Whitehead, E. Lalanne, N. Leyva, I. Konidari, R. C. Gentry, W. F. Hulme, D. Van Booven, D. J. Hedges, V. Mayo, S. S. Ramsook, B. A. Barrionuevo, J. M. Jaworski, M. A. Schmidt, J. L. Haines, M. L. Cuccaro, J. R. Gilbert, M. A. Pericak-Vance.

The discovery and validation of genes recurrently disrupted in autism spectrum disorders. B. J. O’Roak, L. Vives, A. Kumar, I. B. Stanaway, J. Egertson, E. Turner, C. Lee, G. L. Carvil, I. G. Phelps, D. R. O’Day, W. Fu, J. Hiatt, B. Martin, N. Krumm, B. P. Coe, R. Levy, E. Borenstein, D. A. Nickerson, H. C. Mefford, D. Doherty, J. M. Akey, R. Bernier, E. E. Eichler, J. A. Shendure.

Rare complete human knockouts: Population distribution and significant role in autism spectrum disorders. E. T. Lim, M. J. Daly, ARRA Autism Sequencing Consortium.

Exome-based discovery of CNVs in simplex autism families. N. Krumm, B. Nelson, S. Girirajan, M. Dennis, C. Baker, M. Malig, NHLBI Exome Sequencing Project, A. Quinlan, D. A. Nickerson, E. E. Eichler.

Testing for rare variant associations in the presence of missing data. P. Livermore Auer, S. Leal, G. Wang, NHLBI Exome Sequencing Project.

Exome sequencing of more than 6,700 samples and the study of genetic susceptibility to common cancer. A. Kiezun, A. McKenna, G. Kryukov, G. Getz.

Exome sequencing of families severely affected with breast cancer suggests eight new candidate genes: ATR, BAP1, CHEK1, GEN1, KANK4, OBSL1, RAD51B and TP53BP1. C. H. Spurrell, A. M. Thornton, M. K. Lee, S. Casadei, S. Ng, T. Walsh, J. Shendure, M.-C. King.

Exome sequencing in families at high risk for lymphoid malignancies. L. R. Goldin, M. L. McMaster, M. Rotunno, K. B. Jacobs, L. Burdette, M. Malasky, A. Hutchinson, M. Cullen, J. Boland, M. Yeager, M. A. Tucker, S. J. Chanock, N. E. Caporaso.

Enhanced exome sequencing to capture genome-wide common variants. I. C. R. M. Kolder, K. I. Morley, E. Birney, I. Dunham, J. C. Barrett.

Whole exome sequencing identifies candidate causal genes for severe insulin resistance. F. Payne, A. Daly, W. Bottomley, E. Raffan, E. Goncalves Serra, A. Thompson, D. B. Savage, R. K. Semple, S. O’Rahilly, I. Barroso, UK10K Consortium.

Exome analysis in 8,232 Finnish men identifies novel loci and low-frequency variants for insulin processing and secretion. J. R. Huyghe, A. U. Jackson, M. P. Fogarty, A. Stan?áková, H. M. Stringham, M. L. Buchkovich, C. Fuchsberger, J. Paananen, P. S. Chines, T. M. Teslovich, J. M. Romm, H. Ling, I. McMullen, R. Ingersoll, E. W. Pugh, K. F. Doheny, J. Kuusisto, L. J. Scott, F. S. Collins, G. R. Abecasis, R. M. Watanabe, M. Boehnke, M. Laakso, K. L. Mohlke.

Identifying inherited autism mutations using whole exome sequencing. T. W. Yu, M. H. Chahrour, M. E. Coulter, S. Jiralerspong, K. Okamura-Ikeda, K. Schmitz-Abe, G. H. Mochida, J. N. Partlow, R. S. Hill, M. Al-Saffar, N. M. Mukaddes, A. Hashmi, S. Balkhy, G. G. Gascon, O. Oner, S. Al-Saad, T. Ben-Omran, L. Al-Gazali, V. Eapen, C. Stevens, S. Gabriel, K. Markianos, H. Taniguchi, N. E. Braverman, E. M. Morrow, C. A. Walsh.

Whole-exome sequencing for autosomal recessive non-syndromic deafness: 93% of known genes covered and OTOGL and SLITRK6 are novel genes. M. Tekin, O. Diaz-Horta, D. Duman, J. Foster II, A. Sirmaci, M. Gonzalez, N. Mahdieh, M. Bonyadi, F. B. Cengiz, R. Ulloa, S. Zuchner, S. Blanton.

Whole exome sequencing and more to unravel the genetics and genotype-phenotype correlations for deafness. H. Kremer, M. Schraders, C. Zazo Seco, J. Oostrik, I. Feenstra, A. M. M. Oonk, E. van Beelen, M. van Bers, K. Neveling, J. A. Veltman, R. J. C. Admiraal, H. P. M. Kunst, R. J. E. Pennings, E. H. Hoefsloot.

ASHG 2012: Thursday, November 8

My46: An innovative web-based approach to managing and returning results from exome and whole genome sequencing. H. K. Tabor. Seattle Children’s Hosp.

Approaches and attitudes on return of WGS/WES results. K. Ormond. Stanford Univ.

Next steps in development of best practices for use of genome sequencing in clinical care. . A. McGuire. Baylor Col. of Med.

Fine-mapping linkage of age-related traits using whole-exome sequencing in a midwestern Amish population sample. W. K. Scott. Univ. of Miami.

Rare variant extensions of the transmission disequilibrium test detects associations with autism exome sequence data. Z. He, B. O’Road, J. Smith, G. Wang, M. Kan, S. Hooker, B. Li, N. Krumm, D. Nickerson, E. Eichler, S. Leal.

Diagnostic exome sequencing in patients with intellectual disability of unknown cause. J. de Ligt, M. H. Willemsen, B. W. M. van Bon, T. Kleefstra, H. G. Yntema, T. Kroes, A. T. Vulto-van Silfhout, D. A. Koolen, P. de Vries, C. Gilissen, A. Hoischen, H. Scheffer, B. B. A. de Vries, H. G. Brunner, J. A. Veltman, L. E. L. M. Vissers.

Exome sequencing in X-linked intellectual disability family assess the role of the KIAA2022gene in the etiology of intellectual disability. M. Rio, S. Mouton, AC. Mazery, C. Bole-Feysot, P. Nitschke, N. Bahi-Buisson, A. Munnich, L. Colleaux.

Identification of novel mechanisms of drug resistance in BRCA1-deficient cancer by exome and RNA sequencing. K. K. Dhillon, T. Taniguchi.

African American attitudes toward exome and whole genome sequencing. J. Yu, J. Crouch, S. M. Jamal, H. K. Tabor, M. J. Bamshad.

Deep exome sequencing of psoriasis identified new association signals contribute by INDELs, CNVs and rare SNPs. X. Jin, H. Tang, H. Jiang, D. Cao, H. Shao, Q. Li, J. Shen, L. Song, Y. Shi, J. Mei, X. Yang, L. Coin, Y. Li, X. Zhang, J. Wang.

Whole-exome sequencing of 10,000 type 2 diabetes cases and controls from five major ancestry groups. T. M. Teslovich, A. P. Morris, P. Fontanillas, M. A. Rivas, X. Sim, J. Flannick, N. Burtt, H. Chen, A. G. Day-Williams, A. Mahajan, G. Atzmon, P. Cingolani, L. Moutsianas, H. M. Highland, T2D-GENES Consortium.

Rare and low frequency coding variants are associated with LDL cholesterol levels: Findings from the NHLBI Exome Sequencing Project. L. A. Lange, Y. Hu, C. Xue, Z. Tang, C. Bizon, E. M. Lange, J. D. Smith, E. H. Turner, G. Jun, H.-M. Kang, K. P. Li, G. M. Peloso, C. L. Wassel, A. P. Reiner, E. Boerwinkle, B. M. Psaty, C. J. O’Donnell, S. Kathiresan, K. E. North, D. Lin, G. P. Jarvik, L. A. Cupples, C. Kooperberg, J. G. Wilson, D. A. Nickerson, G. R. Abecasis, S. S. Rich, R. P. Tracy, C. J. Willer on behalf of NHLBI Exome Sequencing Project.

Exome sequencing of extreme phenotypes identifies DCTN4 and CAV2 as modifiers of chronicPseudomonas aeruginosa infection in cystic fibrosis. M. J. Emond, T. Louie, J. Emerson, S. McNamara, W. Zhao, R. A. Mathias, M. R. Knowles, F. A. Wright, M. J. Reider, H. K. Tabor, D. A. Nickerson, K. C. Barnes, R. L. Gibson, M. J. Bamshad.

The identification of a novel gene identified by exome sequencing reveals the upstream components of the RAS/MAPK signaling pathway involved in Noonan syndrome. H. Yntema, W. Nillesen, J. Paardekooper Overman, M. Bonetti, J. de Ligt, H. Venselaar, M. Tartaglia, S. G. M. Frints, L. E. L. M. Vissers, J. den Hertog, I. van der Burgt.

Exome sequencing in idiopathic scoliosis reveals rare variants in VANGL, a planar cell polarity gene involved in axial development. S. Sharma, J. A. Herring, X. Gao, D. Zhang, C. Wise.

ASHG 2012: Friday, November 9

The impact of genetic variation on diabetes-related quantitative traits from whole exome sequences: The T2D-GENES Consortium. H. M. Highland, X. Sim, A. Manning, M. Rivas, G. Atzmon, S. Choi, B. K. Cornes, J. Dupuis, J. C. Florez, P. Fontanillas, T. Frayling, E. R. Gamazon, I.-S. Huh, H. K. Im, J. Kim, Y. J. Kim, C. M. Lindgren, A. E. Locke, J. B. Meigs, A. P. Morris, N. Palmer, I. Prokopenko, T. M. Teslovich, T2D-GENES Consortium.

Whole-exome sequencing in multiplex families identifies novel rare variants in multiple sclerosis. A. H. Beecham, J. L. McCauley, A. Hadjixenofontos, P. L. Whitehead, I. Konidari, A. Aviram, Y. Pasco, S. L. Hauser, J. R. Oksenberg, D. J. Hedges, J. M. Vance, J. L. Haines, M. A. Pericak-Vance.

Systematic identification of causal mutations in Mendelian disorders using exome sequence data. M. Lek, N. F. Clarke, L. B. Waddell, B. Thomas, M. A. DePristo, M. J. Daly, K. N. North, D. G. MacArthur.

Exome sequencing of a large cohort of patients with congenital digestive system disorders.M. Yourshaw, S. F. Nelson, M. G. Martín.

Analysis of ESP5400 exomes for results of clinical utility in genes for conditions tested as part of newborn screening programs and age-related macular degeneration. H. K. Tabor, S. M. Jamal, J. H. Yu, A. S. Gordon, W. S. Post, A. D. Johnson, T. A. Graubert, D. A. Nickerson, P. L. Auer, M. J. Bamshad on behalf of NHLBI Personal Genomics Project Team and NHLBI Exome Sequencing Project.

Maximizing detection and minimizing noise: The first report of large scale whole exome sequencing data interpretation in a clinical laboratory. F. Xia, J. Beuten, M. Bainbridge, Z. Niu, M. Vatta, M. R. Bekheirnia, R. E. Person, M. Hardison, J. G. Reid, D. P. Sexton, A. C. Hawes, P. A. Pham, M. Wang, N. Saada, W. Liu, H. Sun, M. Scheel, Y. Ding, A. Roy, J. Wiszniewska, A. Willis, D. M. Muzny, S. E. Plon, J. R. Lupski, A. L. Beaudet, R. A. Gibbs, C. M. Eng, Y. Yang.

Targeted exome sequencing of 102 patients with clinical evidence of mitochondrial disease.D. S. Lieber, S. E. Calvo, K. Shanahan, N. G. Slate, S. Liu, S. G. Hershman, N. B. Gold, B. A. Chapman, M. Borowsky, D. R. Thorburn, G. T. Berry, J. D. Schmahmann, D. M. Mueller, K. B. Sims, V. K. Mootha.

Genetic diagnosis of mitochondrial disorders by whole-exome sequencing. C. J. Carroll, V. Brilhante, P. Isohanni, R. Pöyhönen, L. Euro, U. Richter, T. Lahtinen, A. Götz, H. Almusa, P. Ellonen, H. Pihko, B. Battersby, H. Tyynismaa, A. Suomalainen.

Loss of function mutations in known human disease genes in 572 exomes. J. Johnston, K. Lewis, D. Ng, S. Gonsalves, J. Mullikin, L. G. Biesecker.

Exome sequencing to identify the cause of Mendelian diseases. J. Lupski, C. Gonzaga-Jauregui, W. Wiszniewski, D. Pehlivan, E. Karaca, A. Stray-Pedersen, S. Jhangiani, J. Reid, D. Muzny, R. A. Gibbs, Baylor-Hopkins Center for Mendelian Genomics.

SCID newborn screening and exome sequencing identifies ataxia telangiectasia and low T cells early in life. J. M. Mallott, A. Kwan, J. Church, D. Gonzalez, S. Rana, U. Sunderam, R. Srinivasan, S. E. Brenner, L. F. Tang, F. Lorey, J. Puck.

Exome sequencing results in 230 patients with severe developmental disorders in the DDD project. M. van Kogelenberg, K. Morley, T. Fitzgerald, S. Gerety, A. Tivey, S. Al-Turki, S. Clayton, C. Wright, J. Barrett, H. Firth, D. FitzPatrick, N. Carter, M. Hurles on behalf of DDD Project.

Rare insertion polymorphisms identified by exome sequencing may be associated with age-related macular degeneration. L. Farrer, J. Kozubek, M. Schu, J. Farrell, M. Morrison, K. Mayne, D. Morgan, R. Robinson, A. Swaroop, D. Schaumberg, K.-H. Park, E. E. Tsironi, G. Silvestri, I.-K.. Kim, R. Chen, C. Huff, G. Jun, M. deAngelis.

Whole exome resequencing identifies mutations in LRRC6 as a novel single-gene cause of primary cliary dyskinesia. M. Chaki, H. Y. Gee, E. A. Otto, K. Diaz, T. W. Hurd, J. Halbritter, S. J. Allen, M. B. Zariwala, M. R. Knowles, F. Hildebrandt.

ASHG 2012: Saturday, November 10

Genomic approaches to Mendelian disorders. D. Valle. Johns Hopkins Univ. Sch. of Med.

Current challenges in exome or genome-based analysis of Mendelian disorders. J. Shendure. Univ. of Washington.

Diagnostic implementation of exome sequencing: Results from 500 patients. J. Veltman. Genomic Disorders Nijmegen, Netherlands.

Lessons from 500 diagnostic exomes. H. G. Brunner. Radboud Univ. Nijmegen Med. Ctr., Netherlands.



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