Simultaneous determination of aneuploidy and fetal fraction

Patent metadata

Field	Value
Publication number	US-2022017958-A1
Application number	US-202117465163-A
Country	US
Kind code	A1
Filing date	Sep 2, 2021
Priority date	Jan 19, 2010
Publication date	Jan 20, 2022
Grant date	—

Abstract

The invention provides compositions and methods for simultaneously determining the presence or absence of fetal aneuploidy and the relative amount of fetal nucleic acids in a sample obtained from a pregnant female. The method encompasses the use of sequencing technologies and exploits the occurrence of polymorphisms to provide a streamlined noninvasive process applicable to the practice of prenatal diagnostics.

First claim

What is claimed is:

1 . A method for simultaneously determining fetal aneuploidy and fetal fraction in a maternal blood sample comprising a mixture of fetal and maternal nucleic acid molecules, said method comprising:
(a) enriching said mixture for a plurality of polymorphic target nucleic acids; (b) sequencing at least a portion of the enriched mixture obtained in step (a), wherein said sequencing comprises providing a plurality of sequence tags; and (c) based on said sequencing, simultaneously determining said fetal fraction and said aneuploidy.

2 . The method of claim 1 , wherein said maternal blood sample is the plasma fraction thereof.

3 . The method of claim 1 , wherein said fetal and maternal nucleic acid molecules are cell-free DNA (cfDNA) molecules.

4 . The method of claim 1 , wherein said enriching comprises amplifying a plurality of polymorphic target nucleic acids in a portion of said mixture.

5 . The method of claim 1 , wherein said enriching comprises amplifying a plurality of polymorphic target nucleic acids in a portion of a purified mixture of fetal and maternal nucleic acids.

6 . The method of claim 1 , wherein said enriching comprises combining at least a portion of a first sequencing library of said mixture of fetal and maternal nucleic acid molecules with at least a portion of a second sequencing library of amplified polymorphic target nucleic acids.

7 . The method of claim 1 , wherein said polymorphic target nucleic acids are located on the same or on different chromosomes.

8 . The method of claim 1 , wherein each of said plurality of polymorphic target nucleic acids comprises at least one single nucleotide polymorphism (SNP).

9 . The method of claim 8 , wherein said at least one SNP is a single SNP selected from each of said plurality of polymorphic target nucleic acids comprises a SNP selected from rs560681, rs1109037, rs9866013, rs13182883, rs13218440, rs7041158, rs740598, rs10773760, rs4530059, rs7205345, rs8078417, rs576261, rs2567608, rs430046, rs9951171, rs338882, rs10776839, rs9905977, rs1277284, rs258684, rs1347696, rs508485, rs9788670, rs8137254, rs3143, rs2182957, rs3739005, and rs530022.

10 . The method of claim 8 , wherein said at least one SNP is a tandem SNP.

11 . The method of claim 10 , wherein said tandem SNP is selected from sets of tandem SNPs rs7277033-rs2110153; rs2822654-rs1882882; rs368657-rs376635; rs2822731-rs2822732; rs1475881-rs7275487; rs1735976-rs2827016; rs447340-rs2824097; rs418989-rs13047336; rs987980-rs987981; rs4143392-rs4143391; rs1691324-rs13050434; rs11909758-rs9980111; rs2826842-rs232414; rs1980969-rs1980970; rs9978999-rs9979175; rs1034346-rs12481852; rs7509629-rs2828358; rs4817013-rs7277036; rs9981121-rs2829696; rs455921-rs2898102; rs2898102-rs458848; rs961301-rs2830208; rs2174536-rs458076; rs11088023-rs11088024; rs1011734-rs1011733; rs2831244-rs9789838; rs8132769-rs2831440; rs8134080-rs2831524; rs4817219-rs4817220; rs2250911-rs2250997; rs2831899-rs2831900; rs2831902-rs2831903; rs11088086-rs2251447; rs2832040-rs11088088; rs2832141-rs2246777; rs2832959 -rs9980934; rs2833734-rs2833735; rs933121-rs933122; rs2834140-rs12626953; rs2834485-rs3453; rs9974986-rs2834703; rs2776266-rs2835001; rs1984014-rs1984015; rs7281674-rs2835316; rs13047304-rs13047322; rs2835545-rs4816551; rs2835735-rs2835736; rs13047608-rs2835826; rs2836550-rs2212596; rs2836660-rs2836661; rs465612-rs8131220; rs9980072-rs8130031; rs418359-rs2836926; rs7278447-rs7278858; rs385787-rs367001; rs367001-rs386095; rs2837296-rs2837297; and rs2837381-rs4816672.

12 . The method of claim 1 , wherein each of said plurality of polymorphic target nucleic acids comprises at least one short tandem repeat (STR).

13 . The method of claim 1 , wherein each of said plurality of polymorphic target nucleic acids is an STR selected from CSF1PO, FGA, TH01, TPOX, vWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, D2S1338, Penta D, Penta E, D22S1045, D20S1082, D20S482, D18S853, D17S1301, D17S974, D14S1434, D12ATA63, D11S4463, D10S1435, D10S1248,D9S2157,D9S1122, D8S1115, D6S1017, D6S474, D5S2500, D4S2408, D4S2364, D3S4529, D3S3053, D2S1776, D2S441, D1S1677, D1S1627 and D1GATA113.

14 . The method of claim 12 , wherein said at least one STR is less than about 300 base pairs.

15 . The method of claim 1 , wherein said sequencing is next generation sequencing (NGS).

16 . The method of claim 1 , wherein said sequencing is massively parallel sequencing using sequencing-by-synthesis with reversible dye terminators.

17 . The method of claim 1 , wherein said sequencing is sequencing-by-ligation.

18 . The method of claim 1 , wherein said sequencing comprises an amplification.

19 . The method of claim 1 , wherein said sequencing is single molecule sequencing.

20 . The method of claim 1 , wherein said aneuploidy is a chromosomal aneuploidy.

Assignees

• Verinata Health Inc

Inventors

• Quake Stephen
• Rava Richard P
• Chinnappa Manjula
• Comstock David A
• Heilek Gabrielle

Classifications

• C12Q2545/101

  with an internal standard/control · CPC title

• C12Q1/6872

  involving mass spectrometry · CPC title

• C12Q1/6883

  for diseases caused by alterations of genetic material · CPC title

• C12Q1/6827

  for detection of mutation or polymorphism · CPC title

• C12Q1/68

  involving nucleic acids · CPC title