Tuesday, 25 October 2011

20-30x genome coverage is optimal for whole genome assembly of pyrosequencing data

1. Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data.
Finotello F, Lavezzo E, Fontana P, Peruzzo D, Albiero A, Barzon L, Falda M, Di Camillo B, Toppo S.
Brief Bioinform. 2011 Oct 21. [Epub ahead of print]
PMID: 22021898 [PubMed - as supplied by publisher]


Next-generation sequencing technologies have fostered an unprecedented proliferation of high-throughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads. In this context, an important issue is the need of a careful assessment of the accuracy of the assembly process. Here, we review the efficiency of a panel of assemblers, specifically designed to handle data from GS FLX 454 platform, on three bacterial data sets with different characteristics in terms of reads coverage and repeats content. Our aim is to investigate their strengths and weaknesses in the reconstruction of the reference genomes. In our benchmarking, we assess assemblers' performance, quantifying and characterizing assembly gaps and errors, and evaluating their ability to solve complex genomic regions containing repeats. The final goal of this analysis is to highlight pros and cons of each method, in order to provide the final user with general criteria for the right choice of the appropriate assembly strategy, depending on the specific needs. A further aspect we have explored is the relationship between coverage of a sequencing project and quality of the obtained results. The final outcome suggests that, for a good tradeoff between costs and results, the planned genome coverage of an experiment should not exceed 20-30 ×.

2.Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing.
Myllykangas S, Buenrostro JD, Natsoulis G, Bell JM, Ji HP.
Nat Biotechnol. 2011 Oct 23. doi: 10.1038/nbt.1996. [Epub ahead of print]
PMID: 22020387 [PubMed - as supplied by publisher]


We describe an approach for targeted genome resequencing, called oligonucleotide-selective sequencing (OS-Seq), in which we modify the immobilized lawn of oligonucleotide primers of a next-generation DNA sequencer to function as both a capture and sequencing substrate. We apply OS-Seq to resequence the exons of either 10 or 344 cancer genes from human DNA samples. In our assessment of capture performance, >87% of the captured sequence originated from the intended target region with sequencing coverage falling within a tenfold range for a majority of all targets. Single nucleotide variants (SNVs) called from OS-Seq data agreed with >95% of variants obtained from whole-genome sequencing of the same individual. We also demonstrate mutation discovery from a colorectal cancer tumor sample matched with normal tissue. Overall, we show the robust performance and utility of OS-Seq for the resequencing analysis of human germline and cancer genomes.

3.Integrating Molecular Mechanisms and Clinical Evidence in the Management of Trastuzumab Resistant or Refractory HER-2+ Metastatic Breast Cancer.
Wong H, Leung R, Kwong A, Chiu J, Liang R, Swanton C, Yau T.
Oncologist. 2011 Oct 21. [Epub ahead of print]
PMID: 22020213 [PubMed - as supplied by publisher]
4.Myogenic conversion and transcriptional profiling of embryonic blastomeres in Caenorhabditis elegans.
Fukushige T, Krause M.
Methods. 2011 Oct 13. [Epub ahead of print]
PMID: 22019720 [PubMed - as supplied by publisher]
5.High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing.
Sims D, Mendes-Pereira AM, Frankum J, Burgess D, Cerone MA, Lombardelli C, Mitsopoulos C, Hakas J, Murugaesu N, Isacke CM, Fenwick K, Assiotis I, Kozarewa I, Zvelebil M, Ashworth A, Lord CJ.
Genome Biol. 2011 Oct 21;12(10):R104. [Epub ahead of print]
PMID: 22018332 [PubMed - as supplied by publisher]

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