Exomes vs Genomes (re-visited)

The paper by Lupski et al in Genome Medicine provides fuel to the perpetual debate of Whole Exome Sequencing (WES) vs Whole Genome Sequencing (WGS). It takes me down the memory lane to my own presentation "Genomes or Exomes: evaluation of cost, time and coverage" at Beyond the Genome 2011 conference. (If you would like [...]

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Mitochondrial Gold Rush

Mitochondrial genomes can be extracted from Whole Exome Sequencing (WES) data as outlined by this paper in Nature methods by Ernesto Picardi & Graziano Pesole. Tools like Mito Seek are now available that gather mitochondrial read sequences from NGS data and perform high throughput sequence analysis. Availability of mitochondrial genomes is important as genomic variation in mitochondria has [...]

Journal Club: Indels in 179 genomes (1000genome data)

The origin, evolution and functional impact of short insertion-deletion variants identified in 179 human genomes Genome Research Finally there is a comprehensive analysis on indels, and of course it is the Next Generation Sequencing data that is driving it. I have my concerns with the biases of NGS technology and analysis along with ensuing false-positives [...]

AGBT 2013 Saturday sessions

Plenary Session: Genomic Technologies Len Pennacchio, Lawrence Berkeley National Laboratory, Chair -- could not take notes on some of the talks and afternoon session 9:00 a.m. – 9:30 a.m. Rebecca Leary, Johns Hopkins Kimmel Cancer Center “Personalized Approaches to Non-invasive Cancer Detection” - personalized analysis of rearranged ends (PARE)-identify structural alterations in solid tumors - [...]

AGBT 2013 Friday sessions

Plenary Session:  Genomic Studies II John McPherson, Ontario Institute for Cancer Research, Chair 9:00 a.m. – 9:30 a.m. Steve Scherer, The Hospital for Sick Children “Whole Genome Sequencing Analysis in Autism” - Autism Spectrum Disorder (ASD) - high heritability, familial clustering & ~4:1 male to female bias (as many candidates on X-chr) - 100+ risk [...]

AGBT13 – Thu 2/21 Evening (Genomic Medicine) session

Concurrent Session: Genomic Medicine George Grills, Cornell University, Chair 7:30 p.m. – 7:50 p.m. * Olivier Elemento, Weill Cornell Medical College “Clonal Architecture and Tumor Evolution in Diffuse Large B Cell Lymphomas” - DLBCL - 25k patients / yr in US; treated with immunochemotherapy (60% cured, 40% relapse) - HTS (PCR + MiSeq) of VDJ [...]

AGBT13 – Thu 2/21 Afternoon session

Missed out on a talk and parts of others (and internet was so poor!): Plenary Session: Clinical Genomics II Sharon Plon, Baylor College of Medicine, Chair 2:45 p.m. – 3:15 p.m. Stephen Kingsmore, Children’s Mercy Hospital “Two Year Experience of Pediatric Genomic Medicine at a Large Children’s Hospital” - In genetic diseases, genome sequence is [...]