Haplotype-assisted accurate non-invasive fetal whole genome recovery through maternal plasma sequencing

BackgroundThe applications of massively parallel sequencing technology to fetal cell-free DNA (cff-DNA) have brought new insight to non-invasive prenatal diagnosis. However, most previous research based on maternal plasma sequencing has been restricted to fetal aneuploidies. To detect specific parentally inherited mutations, invasive approaches to obtain fetal DNA are the current standard in the clinic because of the experimental complexity and resource consumption of previously reported non-invasive approaches.MethodsHere, we present a simple and effective non-invasive method for accurate fetal genome recovery-assisted with parental haplotypes. The parental haplotype were firstly inferred using a combination strategy of trio and unrelated individuals. Assisted with the parental haplotype, we then employed a hidden Markov model to non-invasively recover the fetal genome through maternal plasma sequencing.ResultsUsing a sequence depth of approximately 44X against a an approximate 5.69% cff-DNA concentration, we non-invasively inferred fetal genotype and haplotype under different situations of parental heterozygosity. Our data show that 98.57%, 95.37%, and 98.45% of paternal autosome alleles, maternal autosome alleles, and maternal chromosome X in the fetal haplotypes, respectively, were recovered accurately. Additionally, we obtained efficient coverage or strong linkage of 96.65% of reported Mendelian-disorder genes and 98.90% of complex disease-associated markers.ConclusionsOur method provides a useful strategy for non-invasive whole fetal genome recovery.

[1]  K. Klinger,et al.  PCR quantitation of fetal cells in maternal blood in normal and aneuploid pregnancies. , 1997, American journal of human genetics.

[2]  Jay Shendure,et al.  Noninvasive Whole-Genome Sequencing of a Human Fetus , 2012, Science Translational Medicine.

[3]  P. Baird.  Prenatal Screening and the Reduction of Birth Defects in Populations , 1999, Public Health Genomics.

[4]  Cosmin Deciu,et al.  DNA sequencing of maternal plasma to identify Down syndrome and other trisomies in multiple gestations , 2012, Prenatal diagnosis.

[5]  B. Browning,et al.  A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. , 2009, American journal of human genetics.

[6]  E. W. Morris.  No , 1923, The Hospital and health review.

[7]  R. Snijders,et al.  First-trimester screening for trisomies 21 and 18. , 2004, The New England journal of medicine.

[8]  J. Neilson,et al.  Antenatal screening for Down's syndrome , 2004, BMJ : British Medical Journal.

[9]  Timothy B. Stockwell,et al.  The Diploid Genome Sequence of an Individual Human , 2007, PLoS biology.

[10]  Don L. Armstrong,et al.  High-density genotyping of STAT4 reveals multiple haplotypic associations with systemic lupus erythematosus in different racial groups. , 2009, Arthritis and rheumatism.

[11]  Yama W. L. Zheng,et al.  Maternal Plasma DNA Sequencing Reveals the Genome-Wide Genetic and Mutational Profile of the Fetus , 2010, Science Translational Medicine.

[12]  H. C. Fan,et al.  Noninvasive Prenatal Measurement of the Fetal Genome , 2012, Nature.

[13]  Invasive Prenatal Testing for Aneuploidy , 2009 .

[14]  A. Rudnicka,et al.  First-trimester or second-trimester screening, or both, for Down's syndrome. , 2005, New England Journal of Medicine.

[15]  S. Latt,et al.  Isolation of fetal DNA from nucleated erythrocytes in maternal blood. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[16]  T K Lau,et al.  Quantitative analysis of fetal DNA in maternal plasma and serum: implications for noninvasive prenatal diagnosis. , 1998, American journal of human genetics.

[17]  Yusuke Nakamura,et al.  A SNP in the ABCC11 gene is the determinant of human earwax type , 2006, Nature Genetics.

[18]  Lawrence R. Rabiner,et al.  A tutorial on hidden Markov models and selected applications in speech recognition , 1989, Proc. IEEE.

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

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

[21]  N. Youngson,et al.  Transgenerational epigenetic effects. , 2008, Annual review of genomics and human genetics.

[22]  L. Defrancesco.  Life Technologies promises $1,000 genome , 2012, Nature Biotechnology.

[23]  Huanming Yang,et al.  SNP detection for massively parallel whole-genome resequencing. , 2009, Genome research.

[24]  ACOG Practice Bulletin No. 88, December 2007. Invasive prenatal testing for aneuploidy. , 2007, Obstetrics and gynecology.

[25]  F. Collins,et al.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits , 2009, Proceedings of the National Academy of Sciences.

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

[27]  C. Ding,et al.  Noninvasive prenatal detection of fetal trisomy 18 by epigenetic allelic ratio analysis in maternal plasma: Theoretical and empirical considerations. , 2006, Clinical chemistry.

[28]  A. Mcguire,et al.  Antenatal screening for Down's syndrome. , 1992, Journal of medical screening.

[29]  Y. Kan,et al.  Prenatal diagnosis of sickle cell anaemia and thalassaemia by analysis of fetal cells in maternal blood , 1996, Nature Genetics.

[30]  Dawei Li,et al.  The diploid genome sequence of an Asian individual , 2008, Nature.

[31]  Leonore A. Herzenberg,et al.  Fetal cells in the blood of pregnant women: detection and enrichment by fluorescence-activated cell sorting. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[32]  R. Snijders,et al.  First-trimester screening for trisomies 21 and 18 , 2003 .

[33]  A. Mcguire,et al.  Antenatal Screening for Down's Syndrome , 1997, Journal of medical screening.

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

[35]  Ann Tabor,et al.  RANDOMISED CONTROLLED TRIAL OF GENETIC AMNIOCENTESIS IN 4606 LOW-RISK WOMEN , 1986, The Lancet.

[36]  Derek Y. Chiang,et al.  High-resolution mapping of copy-number alterations with massively parallel sequencing , 2009, Nature Methods.

[37]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[38]  C. Cantor,et al.  Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma , 2008, Proceedings of the National Academy of Sciences.

[39]  N. Niikawa,et al.  A strong association between human earwax-type and apocrine colostrum secretion from the mammary gland , 2007, Human Genetics.

[40]  H. Ellegren,et al.  Insertion-deletion polymorphisms (indels) as genetic markers in natural populations , 2008, BMC Genetics.

[41]  H. Swerdlow,et al.  A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers , 2012, BMC Genomics.

[42]  H. C. Fan,et al.  Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood , 2008, Proceedings of the National Academy of Sciences.