Table 1 Comparison of in silico and in vitro results for 30 putatively aberrant SNPs. Here, the diploid genotype refers to that provided by the SNP array's default software [24], under the assumption of two copies of the SNP. The errors shown are typical in the presence of CNVs. The aberrant genotype here is our algorithm's call. We consider the putative CNV to be validated if the rounded qPCR copy number is less than 2 (for deletions) or greater than 2 (for duplications).

NA10851

rs17525374

GG

G -

1

1.17

Yes

NA10851

rs9542207

TT

T -

1

0.86

Yes

NA10851

rs6601728

GG

G -

1

1.40

Yes

NA10851

rs17133566

CC

C -

1

0.98

Yes

NA10863

rs5751296

CT

CTT

1

2.74

Yes

NA10863

rs17577094

TT

TTT

5

4.27

Yes

NA12707

rs1565516

GG

G -

1

1.95

No

NA12707

rs2013317

GG

GGG

4

6.14

Yes

NA12801

rs2304717

CC

CCC

1

4.29

Yes

NA12801

rs12697975

CC

C -

1

0.84

Yes

NA12801

rs2889833

GG

G -

1

1.24

Yes

NA10851

rs11780672

AA

A -

1

0.76

Yes

NA10863

rs3828886

AA

AAA

8

2.12

No

NA10863

rs3858489

AG

AGG

5

3.40

Yes

NA10863

rs17662235

TT

TTT

7

3.36

Yes

NA10863

rs6994627

AA

A -

1

0.88

Yes

NA10863

rs2604357

GG

G -

1

1.54

No

NA10863

rs10110189

CC

C -

1

0.85

Yes

NA10863

rs2721243

CC

C -

1

1.01

Yes

NA10863

rs737714

No Call

A -

1

0.00

Yes

NA10863

rs7833963

AA

A -

1

1.05

Yes

NA10863

rs4831667

AA

A -

1

0.82

Yes

NA10863

rs7464441

AA

A -

1

1.36

Yes

NA12707

rs1018685

AA

AAA

1

1.59

No

NA12707

rs16993280

No Call

- -

3

0.00

Yes

NA12707

rs361901

AA

A -

4

1.40

Yes

NA12707

rs12170791

CC

C -

2

0.98

Yes

NA12707

rs2532292

AA

AAA

7

4.51

Yes

NA12707

rs2732675

No Call

TTT

10

2.53

Yes

NA12707

rs4822622

CC

C -

1

1.06

Yes