Next‐generation sequencing: ready for the clinics?

Desai AN, Jere A. Next‐generation sequencing: ready for the clinics?

[1]  J. Lupski,et al.  Personal genome research : what should the participant be told? , 2010, Trends in genetics : TIG.

[2]  J. Squire,et al.  Integrated Cytogenetic and High-Resolution Array CGH Analysis of Genomic Alterations Associated with MYCN Amplification , 2011, Cytogenetic and Genome Research.

[3]  David P Bick,et al.  Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease , 2011, Genetics in Medicine.

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

[5]  Anthony R. Dallosso,et al.  Multiple rare nonsynonymous variants in the adenomatous polyposis coli gene predispose to colorectal adenomas. , 2008, Cancer research.

[6]  N. Caruccio,et al.  Optimized library preparation method for next-generation sequencing , 2009 .

[7]  K. Lange,et al.  Prioritizing GWAS results: A review of statistical methods and recommendations for their application. , 2010, American journal of human genetics.

[8]  E. Lyon,et al.  The potential for increased clinical sensitivity in genetic testing for polyposis colorectal cancer through the analysis of MYH mutations in North American patients , 2005, Journal of Medical Genetics.

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

[10]  J. Maguire,et al.  Solution Hybrid Selection with Ultra-long Oligonucleotides for Massively Parallel Targeted Sequencing , 2009, Nature Biotechnology.

[11]  Akhilesh K. Tyagi,et al.  De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification , 2011, DNA research : an international journal for rapid publication of reports on genes and genomes.

[12]  Ralf Herwig,et al.  Targeted high throughput sequencing in clinical cancer Settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity , 2011, BMC Medical Genomics.

[13]  D. Valle,et al.  Characterization of complex chromosomal rearrangements by targeted capture and next-generation sequencing. , 2011, Genome research.

[14]  S. Kohl,et al.  Identification of variants in CNGA3 as cause for achromatopsia by exome sequencing of a single patient. , 2011, Archives of ophthalmology.

[15]  M. Gerstein,et al.  PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data , 2009, Genome Biology.

[16]  Yaniv Erlich,et al.  Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis. , 2011, Genome research.

[17]  Ryan W. Kim,et al.  Carrier Testing for Severe Childhood Recessive Diseases by Next-Generation Sequencing , 2011, Science Translational Medicine.

[18]  Ken Chen,et al.  Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. , 2011, JAMA.

[19]  A. Soutar,et al.  A rare polymorphism in the low density lipoprotein (LDL) gene that affects mRNA splicing. , 2007, Atherosclerosis.

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

[21]  Jiannis Ragoussis,et al.  Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA. , 2012, Genome research.

[22]  Elizabeth T. Cirulli,et al.  Whole-Genome Sequencing of a Single Proband Together with Linkage Analysis Identifies a Mendelian Disease Gene , 2010, PLoS genetics.

[23]  A. Ashworth,et al.  Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines , 2011, BMC Medical Genomics.

[24]  Dan M Roden,et al.  A rare variant in MYH6 is associated with high risk of sick sinus syndrome , 2011, Nature Genetics.

[25]  Shawn W. Polson,et al.  Evaluation of a Transposase Protocol for Rapid Generation of Shotgun High-Throughput Sequencing Libraries from Nanogram Quantities of DNA , 2011, Applied and Environmental Microbiology.

[26]  S. Cummings,et al.  Sequence analysis of BRCA1 and BRCA2: correlation of mutations with family history and ovarian cancer risk. , 1998, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[27]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[28]  E. Wang,et al.  Analysis and design of RNA sequencing experiments for identifying isoform regulation , 2010, Nature Methods.

[29]  David B. Goldstein,et al.  A Genome-Wide Investigation of SNPs and CNVs in Schizophrenia , 2009, PLoS genetics.

[30]  S. Koscielny.  Critical review of microarray-based prognostic tests and trials in breast cancer , 2008, Current opinion in obstetrics & gynecology.

[31]  Juliane C. Dohm,et al.  Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia , 2011, Nature.

[32]  Katharina J Hoff,et al.  The effect of sequencing errors on metagenomic gene prediction , 2009, BMC Genomics.

[33]  Nicholas Navin,et al.  Future medical applications of single-cell sequencing in cancer , 2011, Genome Medicine.

[34]  T. Meitinger,et al.  Cohen syndrome diagnosis using whole genome arrays , 2010, Journal of Medical Genetics.

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

[36]  S. Turner,et al.  Real-time DNA sequencing from single polymerase molecules. , 2010, Methods in enzymology.

[37]  Steven J. M. Jones,et al.  De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data , 2009, Genome Biology.

[38]  S. Salzberg,et al.  TopHat-Fusion: an algorithm for discovery of novel fusion transcripts , 2011, Genome Biology.

[39]  T. Glenn.  Field guide to next‐generation DNA sequencers , 2011, Molecular ecology resources.

[40]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[41]  Sang-Jin Park,et al.  Clinical implementation of whole-genome array CGH as a first-tier test in 5080 pre and postnatal cases , 2011, Molecular Cytogenetics.

[42]  Christopher A Cassa,et al.  Disclosing pathogenic genetic variants to research participants: quantifying an emerging ethical responsibility. , 2012, Genome research.

[43]  Jay Shendure,et al.  Massively parallel exon capture and library-free resequencing across 16 genomes , 2009, Nature Methods.

[44]  Simon C. Potter,et al.  Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls , 2007, Nature.

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

[46]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[47]  Bernard P. Puc,et al.  An integrated semiconductor device enabling non-optical genome sequencing , 2011, Nature.

[48]  Emese Meglécz,et al.  Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing , 2011, BMC Genomics.

[49]  J. Lupski,et al.  Exome capture sequencing identifies a novel mutation in BBS4 , 2011, Molecular vision.

[50]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[51]  Y. Ruan,et al.  Broad Surveys of DNA Viral Diversity Obtained through Viral Metagenomics of Mosquitoes , 2011, PloS one.

[52]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[53]  Raymond K. Auerbach,et al.  The real cost of sequencing: higher than you think! , 2011, Genome Biology.

[54]  Steven J. M. Jones,et al.  Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .

[55]  P. Ng,et al.  Predicting the effects of frameshifting indels , 2012, Genome Biology.

[56]  P. Meltzer,et al.  Detection of Novel Amplicons in Prostate Cancer by Comprehensive Genomic Profiling of Prostate Cancer Cell Lines Using Oligonucleotide-Based ArrayCGH , 2007, PloS one.

[57]  Thomas W. Mühleisen,et al.  Association between genetic variation in a region on chromosome 11 and schizophrenia in large samples from Europe , 2012, Molecular Psychiatry.

[58]  Li Ding,et al.  Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. , 2011, JAMA.

[59]  Emily H Turner,et al.  Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome , 2010, Nature Genetics.

[60]  P. Hall,et al.  Transcriptional consequences of genomic structural aberrations in breast cancer. , 2011, Genome research.

[61]  J. Rothberg,et al.  Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology , 2011, PloS one.

[62]  Yutao Fu,et al.  Whole Methylome Analysis by Ultra-Deep Sequencing Using Two-Base Encoding , 2010, PloS one.

[63]  D. Jackson,et al.  Exome Sequencing Reveals Comprehensive Genomic Alterations across Eight Cancer Cell Lines , 2011, PloS one.

[64]  A. Gnirke,et al.  High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.

[65]  A. Pandey,et al.  Whole-genome sequence assembly of the water buffalo (Bubalus bubalis) , 2011 .

[66]  Francisco M. De La Vega,et al.  Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. , 2009, Genome research.

[67]  H. Steven Wiley,et al.  Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling , 2011, Bioinform..

[68]  Sebastian Bauer,et al.  Identity-by-descent filtering of exome sequence data for disease–gene identification in autosomal recessive disorders , 2011, Bioinform..

[69]  L. Stein.  The case for cloud computing in genome informatics , 2010, Genome Biology.

[70]  Martin Kircher,et al.  Improved base calling for the Illumina Genome Analyzer using machine learning strategies , 2009, Genome Biology.

[71]  A. Albino,et al.  Homozygous loss of the p15INK4B gene (and not the p16INK4 gene) during tumor progression in a sporadic melanoma patient. , 1995, Cancer research.

[72]  Life Technologies,et al.  A map of human genome variation from population-scale sequencing , 2011 .

[73]  L. D. White,et al.  Regional genomic instability predisposes to complex dystrophin gene rearrangements , 2009, Human Genetics.

[74]  Bertram Müller-Myhsok,et al.  Genomewide Association Scan of Suicidal Thoughts and Behaviour in Major Depression , 2011, PloS one.

[75]  Margaret C. Linak,et al.  Sequence-specific error profile of Illumina sequencers , 2011, Nucleic acids research.

[76]  Adam P. DeLuca,et al.  Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing , 2010, Proceedings of the National Academy of Sciences.

[77]  A. Ciccodicola,et al.  Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21 , 2011, PloS one.

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

[79]  Ying Liu,et al.  Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications. , 2011, Discovery medicine.