Whole-genome molecular haplotyping of single cells

Abstract

Conventional experimental methods of studying the human genome are limited by the inability to independently study the combination of alleles, or haplotype, on each of the homologous copies of the chromosomes. We developed a microfluidic device capable of separating and amplifying homologous copies of each chromosome from a single human metaphase cell. Single-nucleotide polymorphism (SNP) array analysis of amplified DNA enabled us to achieve completely deterministic, whole-genome, personal haplotypes of four individuals, including a HapMap trio with European ancestry (CEU) and an unrelated European individual. The phases of alleles were determined at ~99.8% accuracy for up to ~96% of all assayed SNPs. We demonstrate several practical applications, including direct observation of recombination events in a family trio, deterministic phasing of deletions in individuals and direct measurement of the human leukocyte antigen haplotypes of an individual. Our approach has potential applications in personal genomics, single-cell genomics and statistical genetics.

In Principle Method for Noninvasive Determination of the Fetal Genome

“…To confirm that the over-represented parental haplotypes corresponded to the ones inherited by the child, the results here were compared against the recombination events that gave rise to the daughter's chromosomes as determined from previous whole-genome haplotyping experiments of the trio 7 . In most cases, the true recombination events were detected.…”

The deepest differences

“…"Working with small volumes gives you some real technical advantages, " says Quake, whose lab is harnessing microfluidics to develop a technique for single-cell transcriptomics, and has created a device to isolate and sequence single chromosomes 10 .…”

In Principle Method for Noninvasive Determination of the Fetal Genome

“…Given a maternal blood sample, the maternal whole-genome haplotypes can be established by culturing lymphocytes to obtain metaphase cells, followed by the wholegenome haplotyping technique developed previously 7 . Yet paternal information may not be available in many situations.…”

“…was 30%), based on mass measurement of the two genomic DNA samples. These two cell lines were used because the whole-genome personal haplotypes of the three members of this family trio were established using a method we developed recently 7 . Sequencing the mixture on one lane of the flow cell on Illumina's Genome Analyzer II yielded ~20 million reads that mapped uniquely to the genome were obtained, covering ~25% of the accessible portion of the genome (i.e.…”

“…Molecular counting can be achieved by shotgun sequencing and personal haplotyping can be achieved by the whole-genome haplotyping recently developed by our group 7 .…”