Dataset Information

Ultraaccurate genome sequencing and haplotyping of single human cells.

ABSTRACT: Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false-positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (single-stranded sequencing using microfluidic reactors), for accurate single-cell genome sequencing and haplotyping. A microfluidic processor is used to separate the Watson and Crick strands of the double-stranded chromosomal DNA in a single cell and to randomly partition megabase-size DNA strands into multiple nanoliter compartments for amplification and construction of barcoded libraries for sequencing. The separation and partitioning of large single-stranded DNA fragments of the homologous chromosome pairs allows for the independent sequencing of each of the complementary and homologous strands. This enables the assembly of long haplotypes and reduction of sequence errors by using the redundant sequence information and haplotype-based error removal. We demonstrated the ability to sequence single-cell genomes with error rates as low as 10-8 and average 500-kb-long DNA fragments that can be assembled into haplotype contigs with N50 greater than 7 Mb. The performance could be further improved with more uniform amplification and more accurate sequence alignment. The ability to obtain accurate genome sequences and haplotype information from single cells will enable applications of genome sequencing for diverse clinical needs.

SUBMITTER: Chu WK

PROVIDER: S-EPMC5703283 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

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Ultraaccurate genome sequencing and haplotyping of single human cells.

Chu Wai Keung WK Edge Peter P Lee Ho Suk HS Bansal Vikas V Bafna Vineet V Huang Xiaohua X Zhang Kun K

Proceedings of the National Academy of Sciences of the United States of America 20171024 47

Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false-positive calls per genome. Second, relatively short sequence reads contain little to no haplotype inf ...[more]

PMID: 29078313

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Project description:A method to infer genome-wide haplotypes from the analysis of one or two single (human) cells has tremendous applicative value. It would revolutionize not only preimplantation genetic diagnosis of in vitro fertilized human embryos in the clinic, but also animal breeding programs by enabling genome-wide quantitative trait loci selection at the embryonic level. In addition, it allows to further scrutinize drivers of haplotype diversity, mainly meiotic homologous recombination as well as somatic (homologous) recombination processes that occur often during (human) tumorigenesis. We developed a generic approach to type genome-wide single nucleotide polymorphisms in single human cells and to reconstruct genome-wide haplotypes of single or dual cell derived genotypes. Genome-wide sequences of syntenic alleles were determined for EBV-transformed lymphoblastoid cells as well as human blastomeres. To this end, multiple displacement amplified DNA samples of single cells were hybridized to Affymetrix 250K SNP-arrays. Different algorithmic designs were subsequently developed to assess from the single cell-derived SNP-probe intensities the sequence of syntenic alleles and to pinpoint accurately the majority of parental homologous recombination sites using a linkage-based approach. In total 12 amplified single human lymphoblastoid cell DNA samples, 3 amplified single human blastomere DNA samples and 19 non-amplified genomic DNA samples extracted from blood were analyzed by 250K Nsp I SNP arrays (GEO accession number GPL3718). The non-amplified genomic DNA samples extracted from blood were derived from 19 different persons belonging to 4 different families. The sample names of these 19 samples are respectively Family1_Individual1, Family1_mother, Family1_father, Family1_MaternalGrandmother, Family2_Individual2, Family2_mother, Family2_father, Family2_MaternalGrandmother, Family2_MaternalGrandfather, Family3_Individual3, Family3_Individual4, Family3_mother, Family3_father, Family3_MaternalGrandmother, Family3_MaternalGrandfather, Family4_mother, Family4_father, Family4_PaternalGrandmother, Family4_PaternalGrandfather. These 19 non-amplified genomic DNA samples extracted from blood were genotyped using the dynamic model algorithm embedded in the M-bM-^@M-^XGeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)M-bM-^@M-^Y using a homozygous and heterozygous calling threshold of 0.12. The 12 amplified single lymphoblastoid cell DNA samples were derived from Epstein Barr virus transformed lymphoblastoid cell lines (EBV-line) of four different persons. Three amplified single lymphoblastoid cell DNA samples from individual M-bM-^@M-^\Family1_Individual1M-bM-^@M-^], three amplified single lymphoblastoid cell DNA samples from individual M-bM-^@M-^\Family2_Individual2M-bM-^@M-^], three amplified single lymphoblastoid cell DNA samples from individual M-bM-^@M-^\Family3_Individual3M-bM-^@M-^] and three amplified single lymphoblastoid cell DNA samples from individual M-bM-^@M-^\Family3_Individual4M-bM-^@M-^]. The samples names of these 12 are respectively: Family1_Individual1_SingleCell1, Family1_Individual1_SingleCell2, Family1_Individual1_SingleCell3, Family2_Individual2_SingleCell1, Family2_Individual2_SingleCell2, Family2_Individual2_SingleCell3, Family3_Individual3_SingleCell1, Family3_Individual3_SingleCell2, Family3_Individual3_SingleCell3, Family3_Individual4_SingleCell1, Family3_Individual4_SingleCell2, Family3_Individual4_SingleCell3. These 12 amplified single lymphoblastoid cell DNA samples were genotyped using (1) the dynamic model algorithm embedded in the M-bM-^@M-^XGeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)M-bM-^@M-^Y using a homozygous and heterozygous calling threshold of 0.12, (2) the BRLMM algorithm within the M-bM-^@M-^XGenotyping console 3.0.1M-bM-^@M-^Y software (Affymetrix) using a scoring threshold of 0.1 and (3) the Birdseed algorithm of the APT-1.10.1 package (Affymetrix Power Tools) using the M-bM-^@M-^Xbirdseed-devM-bM-^@M-^Y command which is the most recently incorporated development version of birdseed from The Broad Institute (http://www.broadinstitute.org/mpg/birdsuite/birdseed.html). The 3 amplified single human blastomere DNA samples were derived from three different human blastomeres that belong to the same in vitro fertilized embryo. This embryo was conceived in vitro by using sperm of person M-bM-^@M-^\Family4_fatherM-bM-^@M-^] and an oocyte from person M-bM-^@M-^\Family4_motherM-bM-^@M-^]. The sample names of these 3 amplified single blastomere DNA samples are respectively: Family4_Blastomere1, Family4_Blastomere2, Family4_Blastomere3. These 3 amplified single human blastomere DNA samples were genotyped using the dynamic model algorithm embedded in the M-bM-^@M-^XGeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)M-bM-^@M-^Y using a homozygous and heterozygous calling threshold of 0.12.

Dataset Information

Ultraaccurate genome sequencing and haplotyping of single human cells.

Publications

Ultraaccurate genome sequencing and haplotyping of single human cells.

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