GenomeLaser: fast and accurate haplotyping from pedigree genotypes

UNLABELLED We present a software tool called GenomeLaser that determines the haplotypes of each person from unphased high-throughput genotypes in family pedigrees. This method features high accuracy, chromosome-range phasing distance, linear computing, flexible pedigree types and flexible genetic marker types. AVAILABILITY AND IMPLEMENTATION http://www.4dgenome.com/software/genomelaser.html.

[1]  Gonçalo Abecasis,et al.  Genotype-imputation accuracy across worldwide human populations. , 2009, American journal of human genetics.

[2]  Dmitry Pushkarev,et al.  Whole-genome haplotyping using long reads and statistical methods , 2014, Nature Biotechnology.

[3]  Pall I. Olason,et al.  Detection of sharing by descent, long-range phasing and haplotype imputation , 2008, Nature Genetics.

[4]  Andrew C. Adey,et al.  Haplotype-resolved genome sequencing of a Gujarati Indian individual , 2011, Nature Biotechnology.

[5]  Tom Druet,et al.  A Hidden Markov Model Combining Linkage and Linkage Disequilibrium Information for Haplotype Reconstruction and Quantitative Trait Locus Fine Mapping , 2010, Genetics.

[6]  Hongyu Zhao,et al.  HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination , 2005, Bioinform..

[7]  Kui Zhang,et al.  Haplotype-association analysis. , 2008, Advances in genetics.

[8]  Miguel Cruz,et al.  Evaluation of the imputation performance of the program IMPUTE in an admixed sample from Mexico City using several model designs , 2012, BMC Medical Genomics.

[9]  Ross M. Fraser,et al.  A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness , 2014, PLoS genetics.

[10]  Tom Druet,et al.  LINKPHASE3: an improved pedigree-based phasing algorithm robust to genotyping and map errors , 2015, Bioinform..

[11]  J. O’Connell.  Zero‐recombinant haplotyping: Applications to fine mapping using SNPs , 2000, Genetic epidemiology.

[12]  Kui Zhang,et al.  High-resolution whole-genome haplotyping using limited seed data , 2012, Nature Methods.

[13]  Wei Wang,et al.  MaCH‐Admix: Genotype Imputation for Admixed Populations , 2013, Genetic epidemiology.

[14]  Ina Hoeschele,et al.  Haplotyping Methods for Pedigrees , 2009, Human Heredity.

[15]  Kui Zhang,et al.  Practical Consideration of Genotype Imputation: Sample Size, Window Size, Reference Choice, and Untyped Rate. , 2011, Statistics and its interface.

[16]  G. Abecasis,et al.  MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes , 2010, Genetic epidemiology.

[17]  Guan-Hua Huang,et al.  Genotype imputation accuracy with different reference panels in admixed populations , 2014, BMC Proceedings.

[18]  Kui Zhang,et al.  Direct determination of molecular haplotypes by chromosome microdissection , 2010, Nature Methods.

[19]  Katja Nowick,et al.  A comprehensively molecular haplotype-resolved genome of a European individual. , 2011, Genome research.

[20]  L Kruglyak,et al.  Parametric and nonparametric linkage analysis: a unified multipoint approach. , 1996, American journal of human genetics.

[21]  Xin Li,et al.  An Almost Linear Time Algorithm for a General Haplotype Solution on Tree Pedigrees with no Recombination and its Extensions , 2009, J. Bioinform. Comput. Biol..

[22]  Zhaohui S. Qin,et al.  Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. , 2002, American journal of human genetics.

[23]  B. Browning,et al.  Haplotype phasing: existing methods and new developments , 2011, Nature Reviews Genetics.

[24]  K Lange,et al.  Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker-sharing statistics. , 1996, American journal of human genetics.

[25]  Bing Ren,et al.  Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing , 2013, Nature Biotechnology.

[26]  Christian R Marshall,et al.  Sequencing of isolated sperm cells for direct haplotyping of a human genome , 2013, Genome research.

[27]  M. Boehnke,et al.  Loss of information due to ambiguous haplotyping of SNPs , 1999, Nature Genetics.

[28]  Wei Chen,et al.  Genotype calling and haplotyping in parent-offspring trios , 2013, Genome research.

[29]  Stephen R Quake,et al.  Whole-genome molecular haplotyping of single cells , 2011, Nature Biotechnology.

[30]  Wing Hung Wong,et al.  Completely phased genome sequencing through chromosome sorting , 2010, Proceedings of the National Academy of Sciences.

[31]  Zhaohui S. Qin,et al.  Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. , 2002, American journal of human genetics.

[32]  G. Abecasis,et al.  Merlin—rapid analysis of dense genetic maps using sparse gene flow trees , 2002, Nature Genetics.

[33]  Wei Xu,et al.  Accurate Inference of Local Phased Ancestry of Modern Admixed Populations , 2014, Scientific reports.