The effect of next-generation sequencing technology on complex trait research

Eur J Clin Invest 2011; 41 (5): 561–567

[1]  Michael Brudno,et al.  SHRiMP: Accurate Mapping of Short Color-space Reads , 2009, PLoS Comput. Biol..

[2]  E. Zeggini,et al.  An Evaluation of Statistical Approaches to Rare Variant Analysis in Genetic Association Studies , 2009, Genetic epidemiology.

[3]  P. Shannon,et al.  Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing , 2010, Science.

[4]  D. Bentley,et al.  Whole-genome re-sequencing. , 2006, Current opinion in genetics & development.

[5]  Antony V. Cox,et al.  Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing , 2008, Nature Genetics.

[6]  R. Durbin,et al.  Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P

, 2022 .

[7]  Separation and detection of DNA by capillary electrophoresis. , 1988, Journal of chromatography.

[8]  J. Todd,et al.  Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes , 2009, Science.

[9]  Steven M. Johnson,et al.  A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. , 2008, Genome research.

[10]  Tom Royce,et al.  A comprehensive catalogue of somatic mutations from a human cancer genome , 2010, Nature.

[11]  P. Shannon,et al.  Exome sequencing identifies the cause of a Mendelian disorder , 2009, Nature Genetics.

[12]  Ken Chen,et al.  Recurring mutations found by sequencing an acute myeloid leukemia genome. , 2009, The New England journal of medicine.

[13]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[14]  M. Metzker.  Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[15]  Lloyd M. Smith,et al.  Fluorescence detection in automated DNA sequence analysis , 1986, Nature.

[16]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[17]  Louette R. Johnson Lutjens.  Research , 2006 .

[18]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[19]  Emily H Turner,et al.  Targeted Capture and Massively Parallel Sequencing of Twelve Human Exomes , 2009, Nature.

[20]  A. Børresen-Dale,et al.  COMPLEX LANDSCAPES OF SOMATIC REARRANGEMENT IN HUMAN BREAST CANCER GENOMES , 2009, Nature.

[21]  J. Lupski,et al.  The complete genome of an individual by massively parallel DNA sequencing , 2008, Nature.

[22]  S. Batzoglou,et al.  Whole-Genome Sequencing and Assembly with High-Throughput, Short-Read Technologies , 2007, PloS one.

[23]  I. Tikhonova,et al.  Genetic diagnosis by whole exome capture and massively parallel DNA sequencing , 2009, Proceedings of the National Academy of Sciences.

[24]  Irina I. Abnizova,et al.  Statistical Comparison of Methods to Estimate the Error Probability in Short-Read Illumina Sequencing , 2010, J. Bioinform. Comput. Biol..

[25]  Ryan D. Morin,et al.  Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution , 2009, Nature.

[26]  A. Paulus,et al.  Rapid separation and purification of oligonucleotides by high-performance capillary gel electrophoresis. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[27]  S. Browning,et al.  A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic , 2009, PLoS genetics.

[28]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[29]  E. Birney,et al.  A small cell lung cancer genome reports complex tobacco exposure signatures , 2009, Nature.

[30]  Heng Li,et al.  A survey of sequence alignment algorithms for next-generation sequencing , 2010, Briefings Bioinform..

[31]  Ruiqiang Li,et al.  SOAP: short oligonucleotide alignment program , 2008, Bioinform..

[32]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[33]  S. Nelson,et al.  BFAST: An Alignment Tool for Large Scale Genome Resequencing , 2009, PloS one.

[34]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[35]  J. Gern.  The Sequence of the Human Genome , 2001, Science.

[36]  P. Stankiewicz,et al.  Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. , 2010, The New England journal of medicine.

[37]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[38]  K. Mullis,et al.  Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. , 1985, Science.

[39]  J. M. Prober,et al.  A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. , 1987, Science.

[40]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[41]  S. Leal,et al.  Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. , 2008, American journal of human genetics.

[42]  D. Mccormick.  Sequence the Human Genome , 1986, Bio/Technology.

[43]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[44]  C. Hutchison.  DNA sequencing: bench to bedside and beyond , 2007, Nucleic acids research.