Diagnosis of Fanconi Anemia: Mutation Analysis by Next-Generation Sequencing

Table 2

Pathogenic mutation detection through filtering.

Sample^1	Variants (total)	Variants (target genes)	NS/SS^2	Not in dbSNP	FA genes^3	Pathogenic clue^4
Sam 1	2535	1579	58	11	4	1
Sam 2	2659	1700	43	6	1	1
Sam 3	2388	1537	40	5	2	2
Sam 5	2490	1570	49	5	4	2
Sam 6	2081	1362	38	5	3	2
Sam 7	2417	1541	34	0	0	0^5
Sam 8	2267	1416	53	5	3	1
Sam 9	2284	1354	34	4	1	1
Sam 10	2570	1760	51	5	2	1
Sam 11	2277	1491	44	7	2	1

¹Sample 4 is not included in this table, as it is composed of pooled DNA from sample 4a and 4b. Slightly different analysis parameters were used for that sample.
²NS: nonsynonymous, SS, splice site.
³Number of variations remaining after filtering for variations in FA genes only.
⁴pathogenic clues are obtained from in silico analysis using Align-GVGD, Polyphen-2, and SIFT [7–9].
⁵This patient is a carrier for a large deletion and a deep intronic mutation. The large deletion is detectable by a separate tool, and the intronic variation is filtered out at this stage.