Methods and processes for non-invasive assessment of genetic variations

• US 10,482,994 B2
• Filed: 02/28/2013
• Issued: 11/19/2019
• Est. Priority Date: 10/04/2012
• Status: Active Grant

• Current Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Deciu, Cosmin, Dzakula, Zeljko, Mazloom, Amin
• Primary Examiner(s): Woitach, Joseph
• Application Number:
  US13/781,530
• Publication Number:
  US 20140100792A1
• Time in Patent Office: 2,455 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2545/101 with an internal standard/control
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: G16B 20/10 Ploidy or copy number detection
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 30/20 Sequence assembly
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

Claims

1. A computer-implemented method for determining fetal fraction based on a copy number variation in a maternal genome, comprising:

(a) sequencing a test sample from a pregnant female bearing a fetus by a non-targeted massively parallel sequencing process that generates nucleotide sequence reads, the test sample comprising circulating cell-free nucleic acid from (i) a maternal genome and (ii) a fetal genome;

mapping the sequence reads to genomic sections of a reference genome; and

counting the sequence reads mapped to the genomic sections of the reference genome, thereby obtaining counts of sequence reads mapped to the genomic sections of the reference genome;

(b) normalizing, using a microprocessor, the counts mapped to the genomic sections of the reference genome, thereby providing normalized counts for the genomic sections;

(c) identifying a first elevation of the normalized counts for a first set of genomic sections significantly different than a second elevation of the normalized counts for a second set of genomic sections, wherein the first set of genomic sections and the second set of genomic sections are within the same chromosome;

(d) determining a copy number variation in the maternal genome for the first set of genomic sections based on the identified first and second elevations;

(e) determining a categorization for the copy number variation in the maternal genome by comparing the first elevation to expected elevations for predetermined copy number variation categorizations; and

(f) determining, using a microprocessor, a fetal fraction of the circulating cell-free nucleic acid according to the first elevation and a deviation from an expected elevation of normalized counts for the categorization.

2. The method of claim 1, wherein the categorization of the copy number variation in the maternal genome is determined in (e) by comparing the first elevation to an expected elevation range for each of the predetermined copy number variation categorizations.

3. The method of claim 2, wherein each expected elevation range is determined according to an expected elevation for each of the predetermined copy number variation categorizations and an uncertainty value.

4. The method of claim 3, wherein the expected elevation for each of the predetermined copy number variation categorizations is determined according to a normalized reference value (NRV) and an expected elevation constant of each of the predetermined copy number variation categorizations.

5. The method of claim 4, wherein the NRV is determined according to a reference elevation.

6. The method of claim 5, wherein the reference elevation is the second elevation.

7. The method of claim 6, wherein the second elevation is an average, mean or median elevation for the second set of genomic sections.

8. The method of claim 4, wherein the NRV is multiplied by the expected elevation constant.

9. The method of claim 4, wherein the expected elevation constant for a maternal homozygous duplication is 2, a maternal heterozygous duplication is 1.5, a maternal heterozygous deletion is 0.5, and a maternal homozygous deletion is zero.

10. The method of claim 3, wherein the uncertainty value is a standard deviation or MAD.

11. The method of claim 1, wherein the copy number variation in the maternal genome determined in (d) is a maternal duplication or a maternal deletion.

12. The method of claim 11, wherein the categorization for the copy number variation in the maternal genome determined in (e) is chosen from a maternal homozygous duplication, a maternal heterozygous duplication, a maternal heterozygous deletion, and a maternal homozygous deletion.

13. The method of claim 1, wherein the second set of genomic sections includes substantially no copy number variation.

14. The method of claim 1, wherein the fetal fraction is determined as twice the difference between the first elevation and an expected elevation of the copy number variation categorization.

15. The method of claim 1, which comprises repeating (c), (d), (e) and (f) for multiple first elevations, and determining multiple fetal fractions.

16. The method of claim 15, wherein two or more fetal fraction determinations are compared, thereby providing a fraction comparison, and the fetal fraction is determined in (f) according to the fraction comparison.

17. The method of claim 1, further comprising outputting a classification of presence or absence of a fetal chromosome aneuploidy for the test sample according to the normalized counts in (b), when the fetal fraction determined in (f) is at or above a fetal fraction threshold.

18. The method of claim 17, wherein the fetal chromosome aneuploidy is chosen from a chromosome 13 trisomy, a chromosome 18 trisomy, a chromosome 21 trisomy or combination thereof.

19. The method of claim 17, comprising performing a medical procedure comprising amniocentesis or chorionic villus sampling when presence of a fetal chromosome aneuploidy is determined.

20. The method of claim 17, comprising performing a medical procedure consistent with a euploid pregnancy when absence of a fetal chromosome aneuploidy is determined.

21. The method of claim 17, wherein the fetal fraction threshold is about 4%.

22. The method of claim 1, wherein the fetus is a female fetus.

23. The method of claim 1, wherein the sequencing in (a) is performed at about 1-fold coverage.

24. The method of claim 1, wherein the sequencing in (a) is performed at less than 1-fold coverage.