Table 1

CNVs identified in 94 subjects across ~1 Mb targeted sequence

Sample_ID

Region

Chr

Start

End

Class

Size

Call

Targeted bases

Median Ratio

Median Z-score

Median S:N

Median Sample Coverage

Median Lane Coverage


CF175_01

PTEN

chr10

89652825

89653723

Deletion

899

DoC + Seq

281

0.45

-8.58

15.58

196

519

CF682_01

PTEN

chr10

89652825

89653723

Deletion

899

DoC + Seq

281

0.51

-8.63

17.04

148

522

CF1815_01

BRCA2

chr13

32928730

32955289

Triplication

26560a

DoC

10560

1.90

11.16

12.11

649

359

CF804_17

BRCA2

chr13

32940522

32945860

Duplication

5339a

DoC

1702

1.63

6.13

10.15

318.5

272

CF815_02

BRCA2

chr13

32960705

32960735

Homozygous Deletion

31

DoC + Seq

31

0b

na

11.94

0

249

CF605_01

BRCA1

chr17

41200740

41201249

Deletion

510

DoC + Seq

419

0.49

-7.79

14.98

119

312

CF456_01

BRCA1

chr17

41214000

41218359

Duplication

4360a

DoC

2332

1.47

7.06

15.45

277

368

CF163_02

BRCA1

chr17

41219555

41219794

Duplication

240a

DoC

240

0.43

-5.26

9.11

77

264

CF499_01

BRCA1

chr17

41230471

41235875

Duplication

5405a

DoC

4000

1.55

8.35

15.93

391

429

CF682_01

CHEK2

chr22

29092633

29099332

Deletion

6700a

DoC

2570

0.50

-8.16

16.21

108

388


a Size reflects minimum size, as breakpoints are located within flanking repetetive sequence

b For homozygous deletion, no reads are present within region

CNVs identified within high-risk breast and ovarian cancer genes targeted by this experiment. Calls were made via depth of coverage (DoC) and confirmed with partially-mapped read analysis (Seq) where possible.

Nord et al. BMC Genomics 2011 12:184   doi:10.1186/1471-2164-12-184

Open Data