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Table 1 Sample Characteristics.

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

Sample ID

Group

TISSUE ORIGIN

Whole mtDNA SEQUENCING PREVIOUSLY PERFORMED

COMPARATIVE SEQUENCING METHOD

mtDNA Haplogroup

MFP Predicted Haplogroup

Unique or Pathogenic Known Feature

Heteroplasmic variant levels

MitoChip Detection of a priori known feature(s)

MFP MitoChip v2.0 Call Rate (%)

1

Clinical

Blood

No

Common point mutation panel (Baylor)

H

H

None

 

Yes

99.5

2

Clinical

Blood

No

Common point mutation panel (Baylor)

I2

I

Heteroplasmic 3243A > G

84%

Yes

99.7

3

Clinical

Blood

No

DHPLC (Transgenomics)

B2b

R*

None

 

Yes

99.6

4

Clinical

Blood

No

DHPLC (Transgenomics)

R*

R*

None

 

Yes

99.5

5

Clinical

Muscle

No

DHPLC (Transgenomics)

N1b2

N1*

None

 

Yes

99.7

6

Clinical

Muscle

Yes

Sanger (Baylor)

J1c

J

Homoplasmic 10845C > T Heteroplasmic 5049C > T

Not reported

Yes

99.8

7

Clinical

Muscle&

Yes

Sanger (Baylor)

J1c

J

Homoplasmic 12264C > T

100%

Yes

99.6

8

Clinical

Blood&

No

qPCR of heteroplasmic variant (Baylor)

J1c

J

Heteroplasmic 12264C > T

30%

Yes

99.6

9

Clinical

Blood

Yes

Sanger (Baylor)

N1a

N1*

Homoplasmic T insertion between 5537 and 5538

 

Yes

99.8

10

Clinical

Blood

Yes

Sanger (Baylor)

N1b2

N1*

None

 

Yes

99.7

11

Clinical

Blood

Yes

Sanger (Baylor)

W1c

W

Homoplasmic 11204T > C

 

Yes

99.6

12

Clinical

Blood

Yes

Sanger (Baylor)

L1b1a

L0/L1

Homoplasmic 11778G > A

 

Yes

99.5

13

Clinical

Fibroblast Cell Line

Yes

Sanger (Baylor)

H

H

None

 

Yes

99.6

14

Research

Cell line

Yes

Sanger (MPK)

K

L3

5 Kb deletion

 

Yes

N/A

15

Research

Hela Cell Line

Yes

Illumina GAII (JAB)

L3b1a1

L3

None

 

No

99.7

16

Research

Blood

Yes

Sanger (TGS)

V7

V

None

 

Yes

99.7

17

Research

Blood

Yes

Sanger (TGS)

H11

H

Heteroplasmy 9966G > A

20%

No

98.5

18

Research

Blood

Yes

Sanger (TGS)

U4a

U*

Heteroplasmy 1706A > G

25%

No

98.9

19

Research

Blood

Yes

Sanger (TGS)

D5a

L3

None

 

Yes

99.7

20

Research

Blood

Yes

Sanger (TGS)

D5a

L3

None

 

Yes

99.6

21

Research

Blood

Yes

Sanger (TGS)

J1c2

J

Heteroplasmy 12879C > T

45%

Yes

99.7

22

Research

Blood

Yes

Sanger (TGS)

T1a

T

None

 

Yes

99.6

23

Research

Blood

Yes

Sanger (TGS)

U4b3

U*

None

 

Yes

99.8

24

Research

Blood

Yes

Sanger (TGS)

D5c

L3

None

 

Yes

99.6

  1. 13 clinical samples and 11 research samples were analyzed by MitoChip v2.0. Tissue origin, comparative mtDNA genome sequencing methodologies, unique or pathogenic features that characterize particular samples based on a priori sequencing knowledge, variant heteroplasmy levels, as well as MitoChip performance in terms of ability to detect known variants and the call rate achieved using MitoChip Filtering Protocol (MFP) are detailed. The 'mtDNA haplogroup' column details the manually curated haplogroup based on full sequence analysis for each sample. 'MitoSNP predicted haplogroup' was based on a subset of 22 mtDNA positions and generally agreed with manual curation, with the exception of haplogroups B, K, and D that were not properly identified by MitoSNP prediction. &, muscle and blood samples originated from the same subject.
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BMC Bioinformatics

ISSN: 1471-2105

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