Methods and processes for non-invasive assessment of genetic variations

1. A method for determining presence or absence of a chromosome trisomy for a test sample, comprising:

(a) sequencing circulating cell-free nucleic acid for a test sample from a pregnant female by a massively parallel sequencing process, thereby generating sequence reads;

(b) obtaining counts of sequence reads mapped to portions of a reference genome;

(c)(i) normalizing the counts in (b), thereby generating normalized counts, and removing normalized counts associated with one or more filtered portions, thereby yielding filtered normalized counts; or (c)(ii) removing counts associated with one or more filtered portions, and normalizing the counts in portions that were not removed, thereby yielding filtered normalized counts; wherein the one or more filtered portions are selected according to one or more criteria chosen from measure of error, redundant data, non-informative data, portions with overrepresented sequences, portions with underrepresented sequences, and noisy data; and

(d) determining presence or absence of a chromosome trisomy for the test sample according to the filtered normalized counts.

2. The method of claim 1 , wherein the one or more filtered portions are selected according to one or more criteria chosen from portions having no guanosine and cytosine (GC) content, portions consistently receiving no counts, and repeat masking.

3. The method of claim 1 , wherein the measure of error is an R factor.

4. The method of claim 3 , wherein portions of the reference genome having an R factor of about 7% or greater were selected as filtered portions.

5. The method of claim 3 , wherein portions of the reference genome having an R factor of about 7% to about 10% were selected as filtered portions.

6. The method of claim 1 , wherein the normalizing in (c)(i) and (c)(ii) comprises normalizing according to GC content of each of the portions.

7. The method of claim 1 , wherein the chromosome trisomy is a chromosome 21 trisomy.

8. The method of claim 1 , comprising: mapping the sequence reads to the portions of the reference genome, and counting the mapped sequence reads.

9. The method of claim 1 , wherein (c) or (d), or (c) and (d), are implemented by a computer.

10. The method of claim 1 , wherein the one or more filtered portions are selected according to measure of error.

11. The method of claim 1 , wherein the one or more filtered portions are selected according to redundant data.

12. The method of claim 1 , wherein the one or more filtered portions are selected according to non-informative data.

13. The method of claim 1 , wherein the one or more filtered portions are selected according to portions with overrepresented sequences.

14. The method of claim 1 , wherein the one or more filtered portions are selected according to portions with underrepresented sequences.

15. The method of claim 1 , wherein the one or more filtered portions are selected according to noisy data.

16. The method of claim 1 , wherein the chromosome trisomy is a chromosome 13 trisomy, a chromosome 18 trisomy, or a chromosome 21 trisomy.