Mitochondrial genome sequence analysis: A custom bioinformatics pipeline substantially improves Affymetrix MitoChip v2.0 call rate and accuracy

Table 2 Variant discrepancy for calls made on MitoChip v2.0 with MFP bioinformatic analysis compared to other methods of whole mitochondrial genome sequencing.

SAMPLE ID #	Total Discordant Base Calls (Missed/Extra)
6	5 (0/5)
7	2 (1/1)
9	1 (1/0)
10	0 (0/0)
11	0 (0/0)
12	1 (0/1)
13	0 (0/0)
15	0 (0/0)
16	0 (0/0)
19	3 (2/1)
20	10 (2/8)
21	0(0/0)
22	0 (0/0)
23	3 (1/2)
24	4 (1/3)

Discrepant calls between MitoChip v2.0 using our custom MFP bioinformatics algorithm are summarized for each of the 15 study samples for which full mtDNA genome sequencing had been previously performed (samples #14, #17 and #18 were excluded from this comparative analysis due to consistent findings of poor sample quality on multiple analyses). Total number of discrepant calls is detailed, with numbers in parentheses specifying calls missed by MFP-based MitoChip analysis that had been made by standard sequencing, as well as the extra calls made by MFP-based MitoChip analysis that had not been detected by standard sequencing. The specific discordant variants from each sample are catalogued in Additional File 4.

ISSN: 1471-2105