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
– generate personalized biomarkers for the detection of circulating tumor DNA
– Tumor-derived mate-pair library -> somatic rearrangements -> confirmed by PCR in tumor & matched normal
– Application = monitor disease progression, identify residual disease (predict relapse), surgical margins
– Plasma Aneuploidy Score – clearly differentiates normals from colorectal cancer samples (just 10x physical coverage – detect rearrangements)
– 0.75% circulating tumor DNA – 90%+ sensitivity, 99%+ specificity using 1 HiSeq lane

9:30 a.m. – 9:55 a.m.
* Eric Antoniou, Cold Spring Harbor Laboratory
“Increased Read Length and Sequence Quality with Pacific Biosciences Magbead Loading System and a New DNA Polymerase”

– duckweed as Biofuel (40tonnes/acre/yr), .1 ton yields .025tons of ethanol by weight and is ~7.5 gallons a day
– rice genome (470 Mbp) sequenced using the Pacific Biosciences RS sequencer (MagBead loading system) – hybrid de novo assembly with Illumina data
– 10kbp insert library; 9X coverage of the rice genome (mean read length – 3kb, max 21kb)
– mean accuracy mode of single pass long read – 90%, (85-87% for current C2 chemistry)

9:55 a.m. – 10:20 a.m.
* Tim Harkins, Life Technologies
“Ovarian Cancer Evolution: a Tale of Two Paths”

– ovarian cancer 9th leading cancer among women, 5th leading cause of cancer related death, high relapse rate

10:45 a.m. – 11:10 a.m.
* X. Sunney Xie, Harvard University
“Detecting Single Nucleotide and Copy Number Variations of a Single Human Cell by Whole Genome Sequencing”

– Individual cells of identical descent can have different genomes (dynamic changes in DNA) – important to many biological investigations and medical diagnoses
– Single-cell whole-genome amplification methods – exponential amplification bias => low genome coverage
– Multiple Annealing and Looping Based Amplification Cycles (MALBAC) – 93% genome coverage ≥ 1x for a single human cell at 30x mean sequencing depth
– detection of digitized CNV & SNVs – ~76% efficiency for a single cancer cell
– 2.5 single-base substitutions per mitosis in human tumor cell line identified using single cell amplification/sequencing
– circulating tumor cells (CTCs) of same patient show similar CNV; CTCs of lung cancer patients show similar CTC
– clinical trial for pre-implantation genomic screening for IVF using single polar bodies of oocytes
– male’s genome can be phased by seq sperm, female’s genome phased using polar bodies genomes
– 0.1X genome coverage is enough to determine aneuploidy (at 8-cell stage) for MALBAC’s single-cell sequencing in IVF
– anomalous transition/transversion ratio for newly acquired SNVs

11:10 a.m. – 11:35 a.m.
* Jeremy Schmutz, HudsonAlpha Institute
“Evaluating Moleculo Long Read Technology for de novo Whole Genome Sequencing”

– Moleculo Long Read technology – sequencing two complex plant genomes (inbred diploid switchgrass comparator Panicum hallii (600 Mb) and the outbred tetraploid Miscanthus sinensis (~2.3 Gb)
– incldue long, retrotransposon-derived repeats, diverse GC-content and present significant challenges for short-read NGS whole genome shotgun sequencing
– Moleculo reads – 10kb reads (5kb avg), high accuracy (1.26bp error/10k), tunable to genome size/complexity, reduces computational complexity
– limitations = distribution of reads depends on local repetitive content & global repeat freq; illumina based => localized chemistry issues; some amplification bias

11:35 a.m. – 12:00 p.m.
* Jonas Korlach, Pacific Biosciences
“Automated, Non-Hybrid De Novo Genome Assemblies and Epigenomes of Bacterial Pathogens”

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