Non-invasive determination of fetal inheritance of parental haplotypes at the genome-wide scale
AssigneeThe Board of Trustees of the Leland Stanford Junior University
InventorsStephen R. Quake, Hei-Mun C. Fan
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Abstract
The present invention provides a method, device and a computer program for haplotyping single cells, such that a sample taken from a pregnant female, without directly sampling the fetus, provides the ability to non-invasively determine the fetal genome. The method can be performed by determining the parental and inherited haplotypes, or can be performed merely on the basis of the mother's genetic information, obtained preferably in a blood or serum sample. The novel device allows for sequence analysis of single chromosomes from a single cell, preferably by partitioning single chromosomes from a metaphase cell into long, thin channels where a sequence analysis can be performed.
Claims18
A method of non-invasively determining parental haplotypes which are inherited by a fetus, comprising:
- a. obtaining a maternal sample from a female pregnant with at least one fetus, wherein said sample contains DNA from both the pregnant female and the fetus;
- b. determining a paternally inherited haplotype by the steps of:
- i. simultaneously isolating all of the chromosomes from a single metaphase cell of the fetus's father by partitioning said chromosomes into a plurality of channels of a microfluidic device and analyzing each of said chromosomes to determine a set of paternal single nucleotide polymorphisms (SNPs);
- ii. simultaneously isolating all of the chromosomes from a single metaphase cell of the fetus's mother by partitioning said chromosomes into a plurality of channels of a microfluidic device and analyzing each of said chromosomes to determine a set of maternal single nucleotide polymorphisms (SNPs);
- iii. determining all SNPs that are heterozygous in the father and homozygous in the mother to identify at various loci alleles present in the father and absent in the mother, thereby defining each of the father's haplotypes;
- and
- iv. counting a number of representative alleles on each paternal haplotype to determine a representation of the two paternal haplotypes in the maternal sample containing DNA from the pregnant female and the fetus;
- v. comparing the representation of the two paternal haplotypes to obtain a relative representation in the maternal sample containing DNA from the pregnant female and the fetus;
- vi. determining an over-representation ε of one of the two paternal haplotypes in the maternal sample containing DNA from the pregnant female and the fetus;
- and
- vii. correlating said over-representation ε with a paternally inherited haplotype;
- and
- c. determining a maternally inherited haplotype by the steps of:
- i. determining all SNPs that are heterozygous in the fetus's mother;
- and
- ii. identifying alleles present in the mother but absent in the paternally inherited haplotype at each SNP locus to define the mother's haplotypes;
- iii. counting a number of representative alleles on each maternal haplotype to determine a representation of the two maternal haplotypes;
- iv. comparing the representation of the two maternal haplotypes to obtain a relative representation;
- v. determining an over-representation ε of one of the two maternal haplotypes in the maternal sample containing DNA from the pregnant female and the fetus;
- and
- vi. correlating said over-representation ε with a maternally inherited haplotype.
A method of non-invasively determining maternal haplotypes which are inherited by a fetus, comprising:
- a. obtaining a maternal sample from a female pregnant with at least one fetus, wherein said sample contains DNA from both the pregnant female and the fetus;
- b. counting markers in said sample that define each of two maternal haplotypes to determine a representation of the two haplotypes, comprising selecting markers that define two maternal haplotypes by simultaneously isolating all of the chromosomes from a single metaphase cell of the fetus's mother by partitioning said chromosomes into a plurality of channels of a microfluidic device;
- c. comparing the representation of the two maternal haplotypes in the maternal sample containing DNA from the pregnant female and the fetus to obtain a relative representation;
- d. determining an over-representation ε of one of the two haplotypes in the maternal sample containing DNA from the pregnant female and the fetus;
- and
- e. correlating said over-representation ε with an inherited maternal haplotype.
Dependencies are inferred from the claim text.