Methods and processes for non-invasive assessment of genetic variations

1. A system comprising one or more microprocessors and memory,

which memory comprises instructions executable by the one or more microprocessors, and which instructions executable by the one or more microprocessors are configured to:

(a) sum counts of nucleotide sequence reads mapped to a subset of genomic sections in the Y chromosome of a reference genome and compare the summed counts to a median count for genomic sections in the Y chromosome for a test sample from a pregnant female bearing a fetus, thereby generating a comparison, wherein:

the sequence reads are reads of circulating cell-free nucleic acid from the sample;

the subset of genomic sections in the Y chromosome comprises a plurality of genomic sections comprising:

i) genomic sections having a consistent number of count totals greater than or equal to 1 for mapped sequence reads from samples from pregnant females carrying male fetuses;

ii) genomic sections having a consistent number of counts for mapped sequence reads from samples from pregnant females carrying female fetuses; and

iii) genomic sections having a significant and consistent difference of mapped sequence read counts between samples from pregnant females carrying male fetuses and samples from pregnant females carrying female fetuses; and

the subset of genomic sections in the Y chromosome does not include selected genomic sections in the Y chromosome, which selected genomic sections in the Y chromosome, when removed from the subset, result in an increase in a separation gap between male and female fetuses greater than or equal to the value ε=1%; and

(b) determine fetal gender according to the comparison.

2. The system of claim 1 , wherein the instructions executable by the one or more microprocessors are configured to determine a male separator region score (MSRscore) for the number of nucleotide sequence reads mapped to each of the genomic sections in the subset according to Equation A:

MSRscore

⁡

(

S

)

=

∑

m

∈

MSR

⁢

⁢

RAW

⁡

(

b

m

⁡

(

S

)

)

M

⁡

(

S

)

Equation

⁢

⁢

A

wherein S is a sample, MSR is male separator region, RAW is raw sequence read counts, b m is a genomic section in the MSR, and M is median sequence read count.

3. The system of claim 2 , wherein the median sequence read count (M) is a median of raw sequence read count totals greater than or equal to 1 for genomic sections of chromosome Y.

4. The system of claim 2 , wherein the fetal gender is determined as male when the MSRscore is 6.5 or more.

5. The system of claim 2 , wherein the fetal gender is determined as female when the MSRscore is less than 6.5.

6. The system of claim 1 , wherein the genomic sections each are a predetermined length of contiguous nucleotides in the Y chromosome.

7. The system of claim 6 , wherein the genomic sections each are about 50 kb in length.

8. The system of claim 7 , wherein the subset of genomic sections is about 50 genomic sections or less.

9. The system of claim 1 , wherein the subset of genomic sections comprises nucleotide sequences located within the first 28 Mb from the 5′ end of the Y chromosome.

10. The system of claim 1 , wherein the sequence reads mapped to the subset of genomic sections are uniquely mapped sequence reads.

11. The system of claim 1 , wherein fetal gender is determined with an accuracy of at least about 99%.

12. The system of claim 1 , wherein the fetal gender is determined with an accuracy of about 0.9938 or greater at a 95% confidence interval.

13. The system of claim 1 , wherein the no-call rate is about 0.40% or less.

14. The system of claim 1 , wherein the sample is blood, serum or plasma.

15. A system comprising one or more microprocessors and memory,

which memory comprises instructions executable by the one or more microprocessors, and which instructions executable by the one or more microprocessors are configured to:

(a) sum counts of nucleotide sequence reads mapped to a subset of genomic sections in the Y chromosome of a reference genome and compare the summed counts to a median count for genomic sections in the Y chromosome for a test sample from a pregnant female bearing a fetus, thereby generating a comparison, wherein:

the sequence reads are reads of circulating cell-free nucleic acid from the sample;

the subset of genomic sections in the Y chromosome comprises a plurality of genomic sections comprising:

i) genomic sections having a consistent number of count totals greater than or equal to 1 for mapped sequence reads from samples from pregnant females carrying male fetuses;

ii) genomic sections having a consistent number of counts for mapped sequence reads from samples from pregnant females carrying female fetuses; and

iii) genomic sections having a significant and consistent difference of mapped sequence read counts between samples from pregnant females carrying male fetuses and samples from pregnant females carrying female fetuses; and

the median count of genomic sections in the Y chromosome is a median of raw sequence read count totals greater than or equal to 1 in the Y chromosome; and

(b) determine fetal gender according to the comparison.

16. The system of claim 15 , wherein the subset of genomic sections in the Y chromosome does not include selected genomic sections in the Y chromosome, which selected genomic sections in the Y chromosome, when removed from the subset, result in an increase in a separation gap between male and female fetuses greater than or equal to the value ε=1%.

17. The system of claim 15 , wherein the instructions executable by the one or more microprocessors are configured to determine a male separator region score (MSRscore) for the number of nucleotide sequence reads mapped to each of the genomic sections in the subset according to Equation A:

MSRscore

⁡

(

S

)

=

∑

m

∈

MSR

⁢

⁢

RAW

⁡

(

b

m

⁡

(

S

)

)

M

⁡

(

S

)

Equation

⁢

⁢

A

wherein S is a sample, MSR is male separator region, RAW is raw sequence read counts, b m is a genomic section in the MSR, and M is median sequence read count.

18. The system of claim 17 , wherein the fetal gender is determined as male when the MSRscore is 6.5 or more.

19. The system of claim 17 , wherein the fetal gender is determined as female when the MSRscore is less than 6.5.

20. The system of claim 15 , wherein the genomic sections each are a predetermined length of contiguous nucleotides in the Y chromosome.

21. The system of claim 20 , wherein the genomic sections each are about 50 kb in length.

22. The system of claim 21 , wherein the subset of genomic sections is about 50 genomic sections or less.

23. The system of claim 15 , wherein the subset of genomic sections comprises nucleotide sequences located within the first 28 Mb from the 5′ end of the Y chromosome.

24. The system of claim 15 , wherein the sequence reads mapped to the subset of genomic sections are uniquely mapped sequence reads.

25. The system of claim 15 , wherein fetal gender is determined with an accuracy of at least about 99%.

26. The system of claim 15 , wherein the fetal gender is determined with an accuracy of about 0.9938 or greater at a 95% confidence interval.

27. The system of claim 15 , wherein the no-call rate is about 0.40% or less.

28. The system of claim 15 , wherein the sample is blood, serum or plasma.