Methods for the diagnosis of fetal abnormalities
AssigneesThe General Hospital Corporation, GPB Scientific, LLC, Verinata Health, Inc.
InventorsRavi Kapur, Mehmet Toner, Roland Stoughton, Daniel Shoemaker, Ronald W. Davis
Life of this patent
Estimating the term…
Abstract
The present invention relates to methods for detecting, enriching, and analyzing rare cells that are present in the blood, e.g. fetal cells. The invention further features methods of analyzing rare cell(s) to determine the presence of an abnormality, disease or condition in a subject, e.g. a fetus by analyzing a cellular sample from the subject.
Claims37
A method for diagnosing the presence or absence of a fetal aneuploidy in a maternal blood sample including fetal and maternal genomic DNA, the method comprising:
- (a) enriching the maternal blood sample for fetal genomic DNA to produce an enriched sample comprising fetal and maternal genomic DNA;
- (b) obtaining fetal and maternal genomic DNA from the enriched sample;
- (c) conducting whole genome amplification of both the fetal and maternal genomic DNA to obtain amplified fetal and amplified maternal genomic DNA molecules;
- (d) performing ultra-deep sequencing of the amplified fetal and amplified maternal genomic DNA molecules of step (c) to produce partial or complete genome sequences corresponding to the amplified fetal and amplified maternal genomic DNA molecules, wherein the ultra-deep sequencing comprises sequencing at least a million of said amplified fetal and amplified maternal genomic DNA molecules in parallel;
- and
- (e) analyzing the genome sequences of the amplified fetal and amplified maternal genomic DNA molecules of step (d) to count chromosomes without performing a single nucleotide polymorphism (SNP) analysis or a short tandem repeat (STR) analysis and thereby determine the presence or absence of said fetal aneuploidy.
A method for diagnosing the presence or absence of a fetal aneuploidy in a maternal blood sample including fetal and maternal genomic DNA, the method comprising:
- (a) enriching the maternal blood sample for fetal genomic DNA to produce an enriched sample comprising fetal and maternal genomic DNA;
- (b) obtaining fetal and maternal genomic DNA from the enriched sample;
- (c) conducting whole genome amplification of both the fetal and maternal genomic DNA to obtain amplified fetal and amplified maternal genomic DNA molecules;
- (d) performing ultra-deep sequencing of the amplified fetal and amplified maternal genomic DNA molecules of step (c) to produce partial or complete genome sequences corresponding to the amplified fetal and amplified maternal genomic DNA molecules, wherein the ultra-deep sequencing comprises conducting amplification of the amplified fetal and amplified maternal genomic DNA molecules of step (c) to produce at least a million clusters of immobilized fetal and maternal genomic DNA molecules in a flow cell and sequencing the clusters of said DNA molecules simultaneously in a sequencing reaction;
- and
- (e) analyzing the genome sequences of the amplified fetal and amplified maternal genomic DNA molecules of step (d) to count chromosomes without performing a single nucleotide polymorphism (SNP) analysis or a short tandem repeat (STR) analysis and thereby determine the presence or absence of said fetal aneuploidy.
A method for determining the presence or absence of a fetal aneuploidy in a maternal blood sample including fetal and maternal genomic DNA, the method comprising:
- (a) enriching the maternal blood sample for fetal genomic DNA to produce an enriched sample comprising fetal and maternal genomic DNA;
- (b) obtaining fetal and maternal genomic DNA from the enriched sample;
- (c) conducting whole genome amplification of both the fetal and maternal genomic DNA to obtain amplified fetal and amplified maternal genomic DNA molecules;
- (d) performing ultra-deep sequencing of the amplified fetal and amplified maternal genomic DNA molecules of step (c) to produce partial or complete genome sequences corresponding to the amplified fetal and amplified maternal genomic DNA molecules, wherein the ultra-deep sequencing comprises sequencing at least a million of said amplified fetal and amplified maternal genomic DNA molecules in parallel;
- and
- (e) analyzing the genome sequences of the amplified fetal and amplified maternal genomic DNA molecules of step (d) to count chromosomes without determining a ratio of the amounts of maternal to paternal alleles and thereby determine the presence or absence of said fetal aneuploidy.
A method for determining the presence or absence of a fetal aneuploidy in a maternal blood sample including fetal and maternal genomic DNA, the method comprising:
- (a) enriching the maternal blood sample for fetal genomic DNA to produce an enriched sample comprising fetal and maternal genomic DNA;
- (b) obtaining fetal and maternal genomic DNA from the enriched sample;
- (c) conducting whole genome amplification of both the fetal and maternal genomic DNA to obtain amplified fetal and amplified maternal genomic DNA molecules;
- (d) performing ultra-deep sequencing of the amplified fetal and amplified maternal genomic DNA molecules of step (c) to produce partial or complete genome sequences corresponding to the amplified fetal and amplified maternal genomic DNA molecules, wherein the ultra-deep sequencing comprises conducting amplification of the amplified fetal and amplified maternal genomic DNA molecules of step (c) to produce at least a million clusters of immobilized fetal and maternal genomic DNA molecules in a flow cell and sequencing the clusters of said DNA molecules simultaneously in a sequencing reaction;
- and
- (e) analyzing the genome sequences of the amplified fetal and amplified maternal genomic DNA molecules of step (d) to count chrommomes without determining a ratio of the amounts of maternal to paternal alleles and thereby determine the presence or absence of said fetal aneuploidy.
Dependencies are inferred from the claim text.