Jack Chen, Associate Professor

Department of Molecular Biology and Biochemistry
Simon Fraser University

Office: SSB8111
Phone: (778)782-4823
Email: chenn(at)sfu.ca

B.Sc., Fudan University, Shanghai
Ph.D., Chinese Academy of Sciences, Qingdao

DNA sequencing and genotyping methods

SEQUENCING METHODS

Roche 454

Genome Sequencer FLX Titanium Series

Illumina Solexa

HiSeq 2000: Up to 200 Gb per run, 2x100 bp read length, up to 25 Gb per day, two billion paired-end reads/run.

Pacific Biosciences

Pacific Biosciences: 1,000 bp or larger reads in early testing

APPLICATIONS

Sanger APPLICATIONS

Roche 454 APPLICATIONS

High-throughput sequencing of retrotransposon integration provides a saturated profile of target activity in Schizosaccharomyces pombe. (Guo et al., Genome Research, 2010)
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. (Holt et al., Nature Genetics, 2008)
A genome-wide view of the spectrum of spontaneous mutations in yeast. (Lynch et al., PNAS, 2008)
The complete genome of an individual by massively parallel DNA sequencing. (Wheeler et al., Nature, 2008)

Illumina Solexa APPLICATIONS

Whole-genome sequencing of a laboratory-evolved yeast strain (Araya et al., BMC Genomics, 2010)
The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana (Stephan Ossowski et al., Science, 2010)
High-Throughput Genetic Mapping of Mutants via Quantitative Single Nucleotide Polymorphism Typing (Sanzhen Liu et al., Genetics 184:19-26, 2010)
High-throughput sequencing reveals suppressors of Vibrio cholerae rpoE mutations: one fewer porin is enough (Brigid M. Davis et al., Bioinformatics, 2009)
Note: This study discovered suppressors using Solexa sequencing.
Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines (Peter D. Keightley et al., 19:1195-1201, 2009)
A genome-wide view of Caenorhabditis elegans base-substitution mutation processes (Dee R. Denver et al., PNAS, 2009)
Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm (Bombyx)(Qingyou Xia et al., Science 326:(5951)433-436, 2009)
High-throughput genotyping by whole-genome resequencing (Huang et al., Genome Research 19:1068-1076)
Identification of EMS-Induced Mutations in Drosophila melanogaster by Whole-Genome Sequencing (Blumenstiel et al., Genetics 182:25-32, 2009)
De Novo Identification of Single Nucleotide Mutations in Caenorhabditis elegans Using Array Comparative Genomic Hybridization (Maydan et al., Genetics 181:1673-1677, 2009)
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans (Hillier et al., Genome Research, 2009)
High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies (Anjana Srivatsan et al., PLoS Genetics, 2008)
Note: This study improved reference genome, discovered hidden phenotypes, and cloned two suppressors
Whole-genome sequencing and variant discovery in C. elegans (Hillier et al., Nature Methods, 2008)

oaCGH APPLICATIONS

Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization (Maydan et al., Genome Research, 2007)
Note: This study revealed using oaCGH extensive indels in two natural isolates of C. elegans: Hawaiian (CB4856) and Madeiran (JU258).
Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans(Maydan et al., BMC Genomics, 2010)
Note: This study extended a previous study using oaCGH on indels in natural isolates of C. elegans.

BIOINFORMATICS

DATA Formats

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants (Peter J. A. Cock et al., Nucleic Acids Research, 2009)

Mapping & Assembly

[SOAPdenovo] De novo assembly of human genomes with massively parallel short read sequencing (Li et al., Genome Research, 2010) (Li et al., Genome Research, 2010)
[BWA-SW] Fast and accurate long read alignment with Burrows-Wheeler transform (Li and Durbin, Bioinformatics, 2010)
[BWA] Fast and accurate short read alignment with Burrows-Wheeler transform (Li and Durbin, Bioinformatics, 2009)
[mrFAST] Personalized copy number and segmental duplication maps using next-generation sequencing (Alkan et al., Nature Genetics, 2009)
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome (Langmead et al., Genome Biology, 2009)
Overlapping pools for high-throughput targeted resequencing (Snehit Prabhu et al., Genome Research, 2009)
SOAP2: an improved ultrafast tool for short read alignment (Li et al., Bioinformatics, 2009)
[MAQ] Mapping short DNA sequencing reads and calling variants using mapping quality scores (Heng Li et al., Genome Research 18:1851-1858, 2008)
Patternhunter II: highly sensitive and fast homology search. (Li et al., J Bioinform Comput Biol, 2002)
The BLAST-Like Alignment Tool(Kent, Genome Research, 2002)
SSAHA: A Fast Search Method for Large DNA Databases (Ning et al., Genome Research, 2001)
[megaBLAST] A Greedy Algorithm for Aligning DNA Sequences (Zhang et al., Journal of Computational Biology, 2000)

SNP identification

[Atlas-SNP2] A SNP discovery method to assess variant allele probability from next-generation resequencing data (Shen et al., Genome Research, 2010)
[SOAPsnp] SNP detection for massively parallel whole-genome resequencing (Ruiqiang Li et al., Genome Research, 19:1124-1132, 2009)

SV identification

[Methods evaluation] Microindel detection in short-read sequence data (Krawitz et al., Bioinformatics, 2010)
[cnD] Copy number variant detection in inbred strains from short read sequence data (Simpson et al., Bioinformatics, 2010)
[Review] Computational methods for discovering structural variation with next-generation sequencing(Medvedev, et al., Nature Methods, 2009)
[VariationHunter] Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes (Hormozdiari et al., Genome Research, 2009)
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads (Ye et al., Bioinformatic, 2009)
MSB: A mean-shift-based approach for the analysis of structural variation in the genome (Wang et al., Genome Research, 19: 106-117, 2009)
[EWT] Sensitive and accurate detection of copy number variants using read depth of coverage (Yoon et al., Genome Research, 19: 1586-1592, 2009)
Common deletion polymorphisms in the human genome (McCarroll et al., Nature Genetics, 2006)
An initial map of insertion and deletion (INDEL) variation in the human genome (Mills et al., Genome Research, 2006)

Deletion breakpoints characterization

Methods to determine DNA structural alterations and genetic instability. (Wang et al., Methods, 2009)
Mutation Spectra in Fragile X Syndrome Induced by Deletions of CGG7CCG Repeats (Wells, JBC, 2009)
Rare pathogenic microdeletions and tandem duplications are microhomology-mediated and stimulated by local genomic architecture (Vissers et al., Human Molecular Genetics, 2009)
Characterization of deletion breakpoints in patients with dystrophinopathy carrying a deletion of exons 4555 of the Duchenne muscular dystrophy (DMD) geneGenomic breakpoints in deletion of exons 45-55 in DMD (Miyazaki et al., Journal of Human Genetics, 2009)
[Review] Discovery of the Role of Non-B DNA Structures in Mutagenesis and Human Genomic Disorders (Robert Wells, JBC, 2009)
Note: This paper reviews various types of Non-B DNA structures (i.e., all DNA conformations other than the orthodox right-handed Watson-Crick structure including cruciforms, triplexes, slipped structure DNA, quadruplexes, and left-handed Z DNA).
[Review] Non-B DNA Conformations, Genomic Rearrangements, and Human Disease (Bacolla and Wells, JBC, 2008)
Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties (Bacolla et al., Genome Research, 2008)
Small Deletion Variants Have Stable Breakpoints Commonly A ssociated with Alu Elements (Smith et al., PLoS ONE, 2008)
[Meeting Review] Meeting DNA palindromes head-to-head (Gerald Smith, Genes & Development, 2008)
Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13) (Gajecka et al., Genome Research, 2008)
The Fine-Scale and Complex Architecture of Human Copy-Number Variation (Perry et al., Am J Hum Genet, 2008)
Low copy repeats mediate distal chromosome 22q11.2 deletions: Sequence analysis predicts breakpoint mechanisms (Shaikh et al., Genome Research, 2007)
Note: This report examines deletions in the human genome.
homopyrimidine sequences are characteristic of genes expressed in brain and the pseudoautosomal region (Bacolla et al., NAR, 2006)
Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity (Ball et al., Human Mutation, 2005)
Non-B DNA Conformations, Genomic Rearrangements, and Human Disease (Bacolla and Wells, JBC, 2004)
Breakpoints of gross deletions coincide with non-B DNA conformations (Bacolla et al., PNAS, 2004)
Note (Comments by Robert Wells, JBC, 2009): This discovery was profound because it amalgamated the topics of DNA structure with human genetics along with bioinformatics and medicine. Breakpoints had been recognized for years to be important in the etiology of various translocations, but this discovery introduced the concept of non-B DNA conformations as signals for the specific breakpoints. This and subsequent work have revealed that slipped structures, cruciforms, triplexes, tetraplexes, and perhaps other non-B DNA structures, including left-handed Z DNA (Fig. 2), are formed in chromosomes and elicit far-reaching genetic consequences via recombination/repair. Repeating sequences, in their non-B conformations, cause gross genomic rearrangements (translocations, deletions, insertions, inversions, and duplications). These rearrangements are the genetic basis for numerous human genomic diseases, including polycystic kidney disease, adrenoleukodystrophy, follicular lymphomas, and spermatogenic failure. At least 70 diseases fall into this category.
Meta-analysis of indels causing human genetic disease: mechanisms of mutagenesis and the role of local DNA sequence complexity (Chuzhanova et al., Human Mutations, 2003)
Coincidence of synteny breakpoints with malignancy-related d eletions on human chromosome 3 (Kost-Alimova et al, PNAS, 2003)
Double-strand breaks and translocations in cancer. (Elliott and Jasin, Cell Mol Life Sci, 2002)
Molecular Nature of Ultraviolet B Light-induced Deletions in the Murine Epidermis (Horiguchi et al., Cancer Research, 2001)
Short, direct repeats at the breakpoints of deletions of the retinoblastoma gene (Canning and Dryja, PNAS, 1989)
Note: This study identified many unique deletions in the retinoblastoma gene in germline DNA (some are homozygous deletions) and discovered many short, direct repeats at the breakpoints of deletions and argues against the existence of "hotspots" in these deletions. Most of these deletion cases have short insertions with the longest one 80 bp in size. It cites a "slipped mispairing" model to explain the formation of these deletions.
Nonhomologous recombination in mammalian cells: role for short sequence homologies in the joining reaction. (Roth and Wilson, Molecular and Cellular Biology, 1986)
Mechanisms of nonhomologous recombination in mammalian cells. (Roth et al., Molecular and Cellular Biology, 1985)

Lethal mutations in healthy individual

Analysis of human disease genes in the context of gene essentiality (Park et al., Genomics, 2008)
Tumour a fly's perspective (Sutcliffe et al., European Journal of Cancer, 2003)
Of flies and studying human disease in Drosophila (Bernards and Hariharan, Current Opinions in Genetics and Development, 2001)
Genetic suppression of phenotypes arising from mutations in dystrophin-related genes in Caenorhabditis elegans (Gieseler et al., Current Biology, 2000)

Weekly Bioinformatics Workshop Slides

Bora: "How to use WestGrid?", Jan 27, 2010, Slides
Chris: "GBrowse - Generic Genome Browser", Feb 2, 2010, Slides

Jack Chen, Associate Professor

Department of Molecular Biology and Biochemistry Simon Fraser University

DNA sequencing and genotyping methods

MAILING LISTS

REVIEWS

BACKGROUND: C. elegans genotype & phenotype: relevance of genomic variations

SEQUENCING METHODS

Roche 454

Illumina Solexa

Pacific Biosciences

APPLICATIONS

Sanger APPLICATIONS

Roche 454 APPLICATIONS

Illumina Solexa APPLICATIONS

oaCGH APPLICATIONS

BIOINFORMATICS

DATA Formats

Mapping & Assembly

SNP identification

SV identification

Deletion breakpoints characterization

Lethal mutations in healthy individual

Weekly Bioinformatics Workshop Slides

Department of Molecular Biology and Biochemistry
Simon Fraser University