4DGENOME, INC
LITERATURE
1968
Ruggero Ceppellini indicate the products of a single locus in haploid form.
Ceppellini, R., in Advances in Transplantation (Copenhagen: Munksgaard, 1968), p. 195.
1975
Terasaki PI, Mickey MR. HLA haplotypes of 32 diseases. Transplant Rev. 1975;22:105-19. PMID: 46641
EXPERIMENTAL TECHNOLOGIES FOR RESOLVING THE HAPLOTYPES
SINGLE-CHROMOSOME SEQUENCING BASED WHOLE GENOME HAPLOTYPING
Ma L, Xiao Y, Huang H, Wang Q, Rao W, Feng Y, Zhang K, Song Q. Direct determination of molecular haplotypes by chromosome microdissection. Nat Methods. 2010 Apr;7(4):299-301. PMID: 20305652; PMCID: PMC2871314.
Yang H, Chen X, Wong WH. Completely phased genome sequencing through chromosome sorting. Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):12-7. PMID: 21169219; PMCID: PMC3017199.
Fan HC, Wang J, Potanina A, Quake SR. Whole-genome molecular haplotyping of single cells. Nat Biotechnol. 2011 Jan;29(1):51-7. PMID: 21170043; PMCID: PMC4098715.
LONG FRAGMENT READ BASED WHOLE GENOME HAPLOTYPING
Kitzman JO, Mackenzie AP, Adey A, Hiatt JB, Patwardhan RP, Sudmant PH, Ng SB, Alkan C, Qiu R, Eichler EE, Shendure J. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat Biotechnol. 2011 Jan;29(1):59-63. PMID: 21170042; PMCID: PMC3116788.
Duitama J, McEwen GK, Huebsch T, Palczewski S, Schulz S, Verstrepen K, Suk EK, Hoehe MR. Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques. Nucleic Acids Res. 2012 Mar;40(5):2041-53. PMID: 22102577; PMCID: PMC3299995.
Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Haas J, Robasky K, Zaranek AW, Lee JH, Ball MP, Peterson JE, Perazich H, Yeung G, Liu J, Chen L, Kennemer MI, Pothuraju K, Konvicka K, Tsoupko-Sitnikov M, Pant KP, Ebert JC, Nilsen GB, Baccash J, Halpern AL, Church GM, Drmanac R. Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature. 2012 Jul 11;487(7406):190-5. PMID: 22785314; PMCID: PMC3397394.
Kuleshov V, Xie D, Chen R, Pushkarev D, Ma Z, Blauwkamp T, Kertesz M, Snyder M. Whole-genome haplotyping using long reads and statistical methods. Nat Biotechnol. 2014 Mar;32(3):261-266. PMID: 24561555; PMCID: PMC4073643.
SINGLE-CELL OR SPERM BASED HAPLOTYPING
Kirkness EF1, Grindberg RV, Yee-Greenbaum J, Marshall CR, Scherer SW, Lasken RS, Venter JC. Sequencing of isolated sperm cells for direct haplotyping of a human genome. Genome Res. 2013 May;23(5):826-32. PMID: 23282328; PMCID: PMC3638138.
Porubský D, Sanders AD, van Wietmarschen N, Falconer E, Hills M, Spierings DC, Bevova MR, Guryev V, Lansdorp PM. Direct chromosome-length haplotyping by single-cell sequencing. Genome Res. 2016 Nov;26(11):1565-1574. PMID: 27646535; PMCID: PMC5088598.
BARCODE PARTITIONING BASED WHOLE GENOME HAPLOTYPING
Xiao M, Wan E, Chu C, Hsueh WC, Cao Y, Kwok PY. Direct determination of haplotypes from single DNA molecules. Nat Methods. 2009 Mar;6(3):199-201. PMID: 19198595 PMCID: PMC3880790.
Zhang F, Christiansen L, Thomas J, Pokholok D, Jackson R, Morrell N, Zhao Y, Wiley M, Welch E, Jaeger E, Granat A, Norberg SJ, Halpern A, C Rogert M, Ronaghi M, Shendure J, Gormley N, Gunderson KL, Steemers FJ. Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube. Nat Biotechnol. 2017 Jun 26. PMID: 28650462.
HIC-BASED WHOLE GENOME HAPLOTYPING
Selvaraj S, R Dixon J, Bansal V, Ren B. Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nat Biotechnol. 2013 Dec;31(12):1111-8. PMID: 24185094; PMCID: PMC4180835.
TRANSPOSITION BASED WHOLE GENOME HAPLOTYPING
Amini S, Pushkarev D, Christiansen L, Kostem E, Royce T, Turk C, Pignatelli N, Adey A, Kitzman JO, Vijayan K, Ronaghi M, Shendure J, Gunderson KL, Steemers FJ. Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat Genet. 2014 Oct 19. PMID: 25326703; PMCID: PMC4409979.
POLONY-BASED LONG-RANGE HAPLOTYPING
Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM. Long-range polony haplotyping of individual human chromosome molecules. Nat Genet. 2006 Mar;38(3):382-7. PMID: 16493423.
A HYBRID EXPERIMENTAL APPROACH
Mostovoy Y, Levy-Sakin M, Lam J, Lam ET, Hastie AR, Marks P, Lee J, Chu C, Lin C, Džakula Ž, Cao H, Schlebusch SA, Giorda K, Schnall-Levin M, Wall JD, Kwok PY. Nat Methods. 2016 Jul;13(7):587-90. A hybrid approach for de novo human genome sequence assembly and phasing. PMID: 27159086; PMCID: PMC4927370.
SOMATIC CELL HYBRID CONSTRUCTION BASED WHOLE GENOME HAPLOTYPING
Yan H, Papadopoulos N, Marra G, Perrera C, Jiricny J, Boland CR, Lynch HT, Chadwick RB, de la Chapelle A, Berg K, Eshleman JR, Yuan W, Markowitz S, Laken SJ, Lengauer C, Kinzler KW, Vogelstein B. Conversion of diploidy to haploidy. Nature. 2000 Feb 17;403(6771):723-4. PMID: 10693791.
Douglas JA, Boehnke M, Gillanders E, Trent JM, Gruber SB. Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibrium studies. Nat Genet. 2001 Aug;28(4):361-4. PMID: 11443299.
STATISTICAL AND COMPUTATIONAL METHODS FOR RESOLVING THE HAPLOTYPES
HIFI SOFTWARE PACKAGE
Rao W, Ma Y, Ma L, Zhao J, Li Q, Gu W, Zhang K, Bond VC, Song Q. High-resolution whole-genome haplotyping using limited seed data. Nat Methods. 2013 Jan;10(1):6-7. PMID: 23269372; PMCID: PMC3835542.
SHAPEIT SOFTWARE PACKAGE
Delaneau O, Marchini J, Zagury JF. A linear complexity phasing method for thousands of genomes. Nat Methods. 2011 Dec 4;9(2):179-81. PMID: 22138821.
MACH SOFTWARE PACKAGE
Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol. 2010 Dec;34(8):816-34. PMID: 21058334; PMCID: PMC3175618.
IMPUTE2 SOFTWARE PACKAGE
Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 2009 Jun;5(6):e1000529. PMID: 19543373; PMCID: PMC2689936.
BEAGLE SOFTWARE PACKAGE
Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007 Nov;81(5):1084-97. PMID: 17924348; PMCID: PMC2265661.
PHASE SOFTWARE PACKAGE
Stephens M, Smith NJ, Donnelly P. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet. 2001 Apr;68(4):978-89. PMID: 11254454; PMCID: PMC1275651.
OTHER
Excoffier L, Slatkin M. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol. 1995 Sep;12(5):921-7. PMID: 7476138.
USING PEDIGREE GENOTYPES FOR RESOLVING THE HAPLOTYPES
LASER SOFTWARE PACKAGE
Li W, Fu G, Rao W, Xu W, Ma L, Guo S, Song Q. GenomeLaser: fast and accurate haplotyping from pedigree genotypes. Bioinformatics. 2015 Dec 15;31(24):3984-7. PMID: 26286810; PMCID: PMC5013932.
PEDPHASE SOFTWARE PACKAGE
Li J, Jiang T. Efficient inference of haplotypes from genotypes on a pedigree.
J Bioinform Comput Biol. 2003 Apr;1(1):41-69. PMID: 15290781.
THEY DESCRIBED THE PRINCIPLE
Hodge SE, Boehnke M, Spence MA. Loss of information due to ambiguous haplotyping of SNPs. Nat Genet 21:360–361 (1999) PMID: 10192383.
REVIEWS ON HAPLOTYPING TECHNOLOGIES
Snyder MW, Adey A, Kitzman JO, Shendure J. Haplotype-resolved genome sequencing: experimental methods and applications. Nat Rev Genet. 2015 Jun;16(6):344-58. PMID: 25948246.
Focused on experimental technologies for resolving haplotypes.
Browning SR, Browning BL. Haplotype phasing: existing methods and new developments. Nat Rev Genet. 2011 Sep 16;12(10):703-14. PMID: 21921926. PMCID: PMC3217888.
Focused on statistical methods for resolving haplotypes
Andrés AM, Clark AG, Shimmin L, Boerwinkle E, Sing CF, Hixson JE. Understanding the accuracy of statistical haplotype inference with sequence data of known phase. Genet Epidemiol. 2007 Nov;31(7):659-71. PMID: 17922479. PMCID: PMC2291540.
Evaluated the phasing accuracy of statistical haplotype inference approach
Rusk N. One genome, two haplotypes. Nat Methods. 2011 Feb;8(2):107. PMID: 21355116.
Research highlights on experimental haplotyping technologies
Bansal V, Tewhey R, Topol EJ, Schork NJ. The next phase in human genetics. Nat Biotechnol. 2011 Jan;29(1):38-9. doi: 10.1038/nbt.1757. PMID: 21221098.
Research highlights on experimental haplotyping technologies
THEORETICAL BREAKTHROUGHS
Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D. The structure of haplotype blocks in the human genome. Science. 2002 Jun 21;296(5576):2225-9. PMID: 12029063.
Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR, Lee DH, Marjoribanks C, McDonough DP, Nguyen BT, Norris MC, Sheehan JB, Shen N, Stern D, Stokowski RP, Thomas DJ, Trulson MO, Vyas KR, Frazer KA, Fodor SP, Cox DR. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science. 2001 Nov 23;294(5547):1719-23. PMID:11721056.
Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES. High-resolution haplotype structure in the human genome. Nat Genet. 2001 Oct;29(2):229-32. PMID: 11586305.
Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, Ackerman HC, Campbell SJ, Altshuler D, Cooper R, Kwiatkowski D, Ward R, Lander ES. Detecting recent positive selection in the human genome from haplotype structure. Nature. 2002 Oct 24;419(6909):832-7. PMID: 12397357.
Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE, Jiang R, Messer CJ, Chew A, Han JH, Duan J, Carr JL, Lee MS, Koshy B, Kumar AM, Zhang G, Newell WR, Windemuth A, Xu C, Kalbfleisch TS, Shaner SL, Arnold K, Schulz V, Drysdale CM, Nandabalan K, Judson RS, Ruano G, Vovis GF. Haplotype variation and linkage disequilibrium in 313 human genes. Science. 2001 Jul 20;293(5529):489-93. PMID: 11452081.
DATABASES
THE 1000 GENOMES PROJECT (2008 - 2015)
http://www.internationalgenome.org/
It created the largest public catalogue of human variation and genotype data, aimed to find most genetic variants with frequencies of at least 1% in the populations studied
1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. A global reference for human genetic variation. Nature. 2015 Oct 1;526(7571):68-74. PMID: 26432245; PMCID: PMC4750478.
1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD,
Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73. PMID: 20981092; PMCID: PMC3042601.
THE INTERNATIONAL HAPMAP PROJECT
www.hapmap.org
This is a public database of common variation in the human genome. The HapMap Resource has been retired by NCBI on June 16, 2016
Manolio TA, Brooks LD, Collins FS. A HapMap harvest of insights into the
genetics of common disease. J Clin Invest. 2008 May;118(5):1590-605. Review. PMID: 18451988; PMCID:PMC2336881.
International HapMap Consortium, Frazer KA et al., A second generation
human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct
18;449(7164):851-61. PMID: 17943122; PMCID: PMC2689609.
International HapMap Consortium. A haplotype map of the human genome. Nature. 2005 Oct 27;437(7063):1299-320. PMID: 16255080; PMCID: PMC1880871.
Robertson D. Racially defined haplotype project debated. Nat Biotechnol. 2001 Sep;19(9):795-6. PMID: 11533624.
HAPLOTYPE REFERENCE CONSORTIUM
http://www.haplotype-reference-consortium.org/
A large reference panel of human haplotypes that can be used for genotype imputation and phasing
McCarthy S. et al., Haplotype Reference Consortium. A reference panel of 64,976 haplotypes for genotype imputation. Nat Genet. 2016 Oct;48(10):1279-83. PMID: 27548312; PMCID: PMC5388176.
DISEASES AND HAPLOTYPES
Habara AH, Shaikho EM, Steinberg MH. Fetal Hemoglobin in Sickle Cell Anemia: The Arab-Indian Haplotype and New Therapeutic Agents. Am J Hematol. 2017 Jul 24. Review. PMID: 28736939.
Haplotyping germline and cancer genomes with high-throughput linked-read sequencing. Zheng GX, Lau BT, Schnall-Levin M, Jarosz M, Bell JM, Hindson CM, Kyriazopoulou-Panagiotopoulou S, Masquelier DA, Merrill L, Terry JM, Mudivarti PA, Wyatt PW, Bharadwaj R, Makarewicz AJ, Li Y, Belgrader P, Price AD, Lowe AJ, Marks P, Vurens GM, Hardenbol P, Montesclaros L, Luo M, Greenfield L, Wong A, Birch DE, Short SW, Bjornson KP, Patel P, Hopmans ES, Wood C, Kaur S, Lockwood GK, Stafford D, Delaney JP, Wu I, Ordonez HS, Grimes SM, Greer S, Lee JY, Belhocine K, Giorda KM, Heaton WH, McDermott GP, Bent ZW, Meschi F, Kondov NO, Wilson R, Bernate JA, Gauby S, Kindwall A, Bermejo C, Fehr AN, Chan A, Saxonov S, Ness KD, Hindson BJ, Ji HP. Nat Biotechnol. 2016 Mar;34(3):303-11. PMID: 26829319.
Wang Y, Brinton RD. Triad of Risk for Late Onset Alzheimer's: Mitochondrial Haplotype, APOE Genotype and Chromosomal Sex. Front Aging Neurosci. 2016 Oct 4;8:232. eCollection 2016. Review. PMID: 27757081 PMCID: PMC5047907.
Bastien JP, Roy J, Roy DC. Selective T-cell depletion for haplotype-mismatched allogeneic stem cell transplantation. Semin Oncol. 2012 Dec;39(6):674-82. Review. PMID: 23206844.
Zimmermann A, Preynat-Seauve O, Tiercy JM, Krause KH, Villard J. Haplotype-based banking of human pluripotent stem cells for transplantation: potential and limitations. Stem Cells Dev. 2012 Sep 1;21(13):2364-73. Review. PMID: 22559254.
Genovese G, Friedman DJ, Ross MD, Lecordier L, Uzureau P, Freedman BI, Bowden DW, Langefeld CD, Oleksyk TK, Uscinski Knob AL, Bernhardy AJ, Hicks PJ, Nelson GW, Vanhollebeke B, Winkler CA, Kopp JB, Pays E, Pollak MR. Association of trypanolytic ApoL1 variants with kidney disease in African Americans. Science. 2010 Aug 13;329(5993):841-5. PMID: 20647424; PMCID: PMC2980843.
Etzensperger R, McMahon RM, Jones EY, Fugger L. Dissection of the multiple sclerosis associated DR2 haplotype. J Autoimmun. 2008 Nov;31(3):201-7. Review. PMID: 18513924.
Bao X, Mills PJ, Rana BK, Dimsdale JE, Schork NJ, Smith DW, Rao F, Milic M, O'Connor DT, Ziegler MG. Interactive effects of common beta2-adrenoceptor haplotypes and age on susceptibility to hypertension and receptor function. Hypertension. 2005 Aug;46(2):301-7. PMID: 16027244.
Lee JE, Choi JH, Lee JH, Lee MG. Gene SNPs and mutations in clinical genetic testing: haplotype-based testing and analysis. Mutat Res. 2005 Jun 3;573(1-2):195-204. Review. PMID: 15829248.
Panguluri RC, Long LO, Chen W, Wang S, Coulibaly A, Ukoli F, Jackson A, Weinrich S, Ahaghotu C, Isaacs W, Kittles RA. COX-2 gene promoter haplotypes and prostate cancer risk. Carcinogenesis. 2004 Jun;25(6):961-6. PMID: 14754878.
Yu H, Song Q, Freedman BI, Chao J, Chao L, Rich SS, Bowden DW. Association of the tissue kallikrein gene promoter with ESRD and hypertension. Kidney Int. 2002 Mar;61(3):1030-9. PMID: 11849458.
Mikkelsson J, Perola M, Penttilä A, Karhunen PJ. Platelet glycoprotein Ibalpha HPA-2 Met/VNTR B haplotype as a genetic predictor of myocardial infarction and sudden cardiac death. Circulation. 2001 Aug 21;104(8):876-80. PMID:11514372.
Tishkoff SA, Varkonyi R, Cahinhinan N, Abbes S, Argyropoulos G, Destro-Bisol G, Drousiotou A, Dangerfield B, Lefranc G, Loiselet J, Piro A, Stoneking M, Tagarelli A, Tagarelli G, Touma EH, Williams SM, Clark AG. Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science. 2001 Jul 20;293(5529):455-62. PubMed PMID: 11423617.
Thomson G, Bodmer W. HLA haplotype associations with disease. Tissue Antigens. 1979 Feb;13(2):91-102. PMID: 87027.
PHARMACOGENOMICS AND HAPLOTYPES
Mallal S, Nolan D, Witt C, Masel G, Martin AM, Moore C, Sayer D, Castley A, Mamotte C, Maxwell D, James I, Christiansen FT. Association between presence of HLA-B*5701, HLA-DR7, and HLA-DQ3 and hypersensitivity to HIV-1 reverse-transcriptase inhibitor abacavir. Lancet. 2002 Mar 2;359(9308):727-32. PMID: 11888582
Hetherington S, Hughes AR, Mosteller M, Shortino D, Baker KL, Spreen W, Lai E, Davies K, Handley A, Dow DJ, Fling ME, Stocum M, Bowman C, Thurmond LM, Roses AD. Genetic variations in HLA-B region and hypersensitivity reactions to abacavir. Lancet. 2002 Mar 30;359(9312):1121-2. PMID: 11943262.