Identifying and correcting sample mix-ups in high-dimensional data

Salvaging a genetics project Identifying and correcting sample mix-ups in high-dimensional data Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman bit.ly/berkeley2017

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daviddeen.com

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Intercross P1

P2

F1

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F2 4

Data

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QTL mapping

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LOD score

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QTL mapping 1.1

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1.0 0.9 0.8

LOD score

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RR

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Attie project ∼500 B6 × BTBR intercross mice, all ob/ob ▶

Genotypes at 2057 SNPs (Affymetrix arrays)

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Gene expression in six tissues (Agilent arrays) – – – – – –

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adipose gastrocnemius muscle hypothalamus pancreatic islets kidney liver

Numerous clinical phenotypes (e.g., body weight, insulin and glucose levels)

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Sex and the X chr B6

BTBR

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F2

Female

Male 8

Genotype mix-ups 1631

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1629 A B C D E F G H

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B6 ●

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A B C D E F G H

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1632 A B C D E F G H

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A B C D E F G H

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● BTBR ● ●

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A B C D E F G H

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1633

● ● ● BTBR ● ●

1630 1

1628 1 A B C D E F G H

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Sex and the X chr B6

BTBR

F1

F2

Female

Male 10

Strong eQTL 150

probe 499541 (on chr 1)

LOD score

100

50

0 1

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14 15 16 17 18 19

X

Chromosome

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Strong eQTL 150

probe 499541 (on chr 1)

probe 10002916257 (on chr 13)

LOD score

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0 1

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X

Chromosome

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E vs G

expression of 499541

0.0

● ● ●●●● ●● ●●● ● ● ●● ●● ● ●● ● ● ● ●● ● ● ● ● ● ●● ●● ● ● ● ●●● ● ● ● ● ● ●● ● ● ●●●●● ● ●● ● ● ●● ● ● ● ● ● ● ● ●●● ● ● ● ● ●● ● ●● ●● ● ● ● ● ● ● ● ●● ● ● ●●● ● ● ● ● ● ● ●● ● ●

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−0.5

−1.0 ● ● ● ●

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BB

BR

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RR

Genotype at rs13476158

12

E vs G

expression of 499541

0.0

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−1.0 ● ● ● ●

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BB

BR

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RR

Genotype at rs13476158

12

kNN classifier

expression of 499541

0.0

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● ● ●● ● ● ●●● ● ●●● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ●●● ●● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ●● ● ● ●● ● ●● ● ● ● ● ●● ● ● ● ●●● ● ● ● ● ● ● ● ● ●● ●● ●● ●● ●● ●●● ● ● ● ●●●● ● ●

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BB

BR

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RR

Genotype at rs13476158

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E vs G 0.4

Genotype at rs6244221

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RR ● ●●●

expression of 10004035488

BR 0.2

0.0

BB ● ●

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●

● ●

● ● ● ● ●● ● ● ● ● ● ● ●● ● ●●● ● ●●● ● ● ●● ●● ● ● ● ● ● ● ● ● ●● ● ●●●● ●● ● ● ●● ●● ● ● ● ●● ● ● ● ●● ●● ● ● ● ●●●● ● ● ● ● ● ● ● ●● ● ● ●● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●●● ● ● ● ●●● ● ●● ● ● ● ●●●●● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ●●● ● ● ● ● ● ● ●● ●●●●● ●● ● ● ● ● ● ● ● ●● ●● ●● ●●● ● ● ● ●● ● ●● ● ● ● ●●● ●● ●● ● ●● ● ● ● ● ●●● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ●● ● ●●●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●●●●●● ● ● ● ●● ● ● ● ●● ●●●●● ● ●●● ●● ● ● ● ●● ● ● ●●● ● ●●●● ●● ● ●●●●● ● ● ● ●● ● ● ● ●● ● ● ●●●●● ● ●● ●● ● ● ●●

●

●

−0.6 −1.0

−0.5

0.0

expression of 518187

14

E vs G 0.4

Genotype at rs6244221

●

RR ● ●●●

expression of 10004035488

BR 0.2

0.0

BB ● ●

−0.2

●

−0.4

●

● ●

●

●●

●

● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ●● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ●● ● ●●● ● ●● ● ●● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

●

● ●

● ● ● ● ●● ● ● ● ● ● ● ●● ● ●●● ● ●●● ● ● ●● ●● ● ● ● ● ● ● ● ● ●● ● ●●●● ●● ● ● ●● ●● ● ● ● ●● ● ● ● ●● ●● ● ● ● ●●●● ● ● ● ● ● ● ● ●● ● ● ●● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●●● ● ● ● ●●● ● ●● ● ● ● ●●●●● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ●●● ● ● ● ● ● ● ●● ●●●●● ●● ● ● ● ● ● ● ● ●● ●● ●● ●●● ● ● ● ●● ● ●● ● ● ● ●●● ●● ●● ● ●● ● ● ● ● ●●● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ●● ● ●●●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●●●●●● ● ● ● ●● ● ● ● ●● ●●●●● ● ●●● ●● ● ● ● ●● ● ● ●●● ● ●●●● ●● ● ●●●●● ● ● ● ●● ● ● ● ●● ● ● ●●●●● ● ●● ●● ● ● ●●

●

●

−0.6 −1.0

−0.5

0.0

expression of 518187

14

E vs G 0.5

● ● ● ● ●● ● ● ● ● ●● ● ●●●●● ● ● ● ● ●● ● ●● ●● ●● ● ●● ●● ●● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ●● ● ● ● ● ● ●● ● ● ●● ● ● ●● ● ●●● ● ● ● ● ● ●●●●● ●● ●● ● ● ●● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ●●● ● ● ● ● ● ● ● ● ●● ●● ●● ● ●● ●● ● ●● ●●● ● ●● ● ●● ●● ●● ● ● ● ●● ● ●● ● ●● ●●●● ●● ● ●●● ● ●● ● ● ●● ● ● ● ● ● ●● ● ●●● ●● ● ●● ●●●●●● ● ● ● ●●●● ●●●●● ● ●●● ●●●● ● ● ● ●●●●●●●●● ● ●●● ● ● ●●● ● ●● ● ● ●● ● ● ●● ● ● ●●● ●● ● ● ● ● ● ● ●● ●●● ● ●● ● ● ● ● ●● ● ● ● ● ●

Genotype at rs13478402

RR

●

● ●

expression of 502129

●

0.0 ●

● ●

−0.5 ● ●

●

−1.0

● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ●●● ● ● ●● ● ●● ● ●● ● ● ●●●●● ● ● ● ●●● ●● ● ●●● ● ●● ● ● ●● ●●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ●● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●

●

●

BR

● ●

●

BB

●

●●

−0.6

−0.4

−0.2

0.0

0.2

0.4

0.6

expression of 517583

15

E vs G 0.5

● ● ● ● ●● ● ● ● ● ●● ● ●●●●● ● ● ● ● ●● ● ●● ●● ●● ● ●● ●● ●● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ●● ● ● ● ● ● ●● ● ● ●● ● ● ●● ● ●●● ● ● ● ● ● ●●●●● ●● ●● ● ● ●● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ●●● ● ● ● ● ● ● ● ● ●● ●● ●● ● ●● ●● ● ●● ●●● ● ●● ● ●● ●● ●● ● ● ● ●● ● ●● ● ●● ●●●● ●● ● ●●● ● ●● ● ● ●● ● ● ● ● ● ●● ● ●●● ●● ● ●● ●●●●●● ● ● ● ●●●● ●●●●● ● ●●● ●●●● ● ● ● ●●●●●●●●● ● ●●● ● ● ●●● ● ●● ● ● ●● ● ● ●● ● ● ●●● ●● ● ● ● ● ● ● ●● ●●● ● ●● ● ● ● ● ●● ● ● ● ● ●

Genotype at rs13478402

RR

●

● ●

expression of 502129

●

0.0 ●

● ●

−0.5 ● ●

●

−1.0

● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ●●● ● ● ●● ● ●● ● ●● ● ● ●●●●● ● ● ● ●●● ●● ● ●●● ● ●● ● ● ●● ●●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ●● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●

●

●

BR

● ●

●

BB

●

●●

−0.6

−0.4

−0.2

0.0

0.2

0.4

0.6

expression of 517583

15

Basic scheme

mice

expression traits

transcripts

mice

observed eQTL genotypes

eQTL

16

Basic scheme

mice

expression traits

inferred eQTL genotypes

mice

transcripts

observed eQTL genotypes

mice

eQTL

eQTL

16

Basic scheme

mice

expression traits

inferred eQTL genotypes

mice

transcripts

observed eQTL genotypes

mice

eQTL

eQTL

16

Basic scheme

mice

expression traits

inferred eQTL genotypes

mice

transcripts

observed eQTL genotypes

mice

eQTL

eQTL

16

Prop’n mismatches

17

Prop’n mismatches 100

80 1.0

mRNA sample

0.8 60 0.6 0.4 40 0.2 0.0 20

1 1

20

40

60

80

100

DNA sample

18

Prop’n mismatches 300

280 1.0

mRNA sample

0.8 260 0.6 0.4 240 0.2 0.0 220

201 201

220

240

260

280

300

DNA sample

19

Prop’n mismatches Self−self

0.0

0.2

0.4

0.6

0.8

1.0

Proportion of mismatches

Self−nonself

0.0

0.2

0.4

0.6

0.8

1.0

Proportion of mismatches

20

Decisions Self vs best ●

0.8

self−self distance

0.6

Fixable

● ●●

●

● ● ● ●● ● ● ● ● ●● ● ●● ● ● ●● ● ● ●● ● ●● ● ●● ● ● ●● ●●● ● ●● ●●●● ● ●●

Not found ●

● ●●

● ●

● ● ●

●●● ● ● ● ● ●● ● ● ●● ● ●● ●●● ● ● ●

●

● ●

0.4

0.2

● ●

0.0

● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

0.0

Good

0.2

0.4

0.6

0.8

minimum distance

21

Genotype mix-ups 1631

1634 A B C D E F G H

1

2

3

4

5

6

7

8

9

10 11 12

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

●

● ●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

●

●

● ●

● ●

● ●

● ●

●

● ●

● ●

● ●

● ●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

1629 A B C D E F G H

1

2

3

4

5

6

7

8

9

10 11 12

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

●

● ●

● ●

● ●

● ●

● ●

● ●

B6 ●

● ●

● ●

● ●

● ●

●

● ●

● ●

● ●

● ●

● ●

● BTBR ● ● ● ●

● ●

● ●

● ●

●

A B C D E F G H

1

2

3

4

5

6

7

8

9

10 11 12

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

F1 ●

● ●

●

● ●

● ●

●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

● ●

● ●

● ●

● ●

● ●

● ●

●

● ●

● ●

● ●

● ●

●

● ●

● ●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

1632 A B C D E F G H

1

2

3

4

5

6

7

8

9

10 11 12

●

● ●

● ●

● ●

● ●

● ●

● ●

●

●

●

●

●

● ●

● ●

● ●

●

● ●

● ●

● ●

●

●

●

●

●

●

● ●

● ●

● ●

● ●

● ●

● ●

●

●

●

●

●

●

● ●

● ●

●

● ●

● ●

●

●

●

●

●

●

●

● ●

●

● ●

● ●

● ●

● ●

●

●

●

●

●

● ●

● ●

●

● ●

● ●

● ●

●

●

●

●

●

● ●

● ●

● ●

● ●

● ●

●

●

●

● ●

●

●

● ●

● ●

● ●

●

●

●

A B C D E F G H

2

3

4

5

6

● BTBR ● ●

7

8

9

10 11 12

●

● ●

● ●

● ●

● ●

●

●

●

●

●

●

●

●

●

●

●

●

●

● ●

● ●

●

●

●

●

●

● ● ● ● ● BTBR ● ●

● ●

●

●

● ●

● ●

●

● ●

● ●

● ●

● ●

●

●

●

●

●

●

●

F1 ●

●

●

●

●

●

●

●

● ●

● ●

● ●

● ●

●

●

●

●

●

●

●

●

● ●

● ●

● ●

● ●

●

● ●

● ●

● ●

●

● ●

● ●

● ●

●

●

●

●

●

●

●

●

● ●

●

●

●

●

●

●

●

● ●

2

3

4

5

6

7

8

9

10 11 12

B6 ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

B6 ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

● ●

●

● ●

● ●

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1

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10 11 12

A B C D E F G H

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1633

● ● ● BTBR ● ●

1630 1

1628 1 A B C D E F G H

22

Plate 1631

23

Plates 1632 and 1630

24

Plate 1630

25

E vs E

mice

expression in islet

transcripts

mice

expression in liver

transcripts

26

E vs E

mice

expression in islet

transcripts

mice

expression in liver

transcripts

27

E vs E

28

E vs E

mice

expression in islet

transcript 497973 transcripts

expression in liver

liver expression

2

● ● ● ● ● ● ●● ● ● ● ● ● ●●● ● ● ● ●●●● ● ● ● ● ● ●● ● ●●●●● ●● ● ● ● ● ● ●● ●● ●● ● ● ●● ●● ●●●● ● ● ●● ● ● ●● ● ●●● ● ● ● ● ●● ●●● ●●●● ● ● ● ● ● ● ● ●●● ● ● ● ● ●●● ● ●●● ●●●●● ●●● ●● ● ● ●● ● ● ●● ●●●●● ● ●● ●● ● ●●● ●● ● ●● ● ● ●● ●● ● ●●● ●● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ●●●● ●●●● ●●●● ● ● ● ●● ● ●● ●●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●●●● ● ● ● ●● ●● ●● ● ● ● ●●● ●● ●● ●● ● ● ●● ●● ● ●● ● ● ● ● ●● ● ●● ● ●● ● ●● ● ●● ●●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ●●● ● ● ●●● ●● ● ●● ● ●● ● ● ● ●● ●● ●● ●● ● ● ● ● ● ● ● ●●● ● ● ●● ● ● ● ●● ● ● ●● ●● ●● ●● ● ●● ● ● ●● ●● ●● ● ●● ● ● ●●●● ● ●● ●● ● ●● ●● ●●● ● ● ●● ● ● ●● ●● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ●●●● ● ●● ●● ●● ●● ● ● ● ● ● ●● ●

●

1 0 −1 −2

●

●

● ●

●

−3 −4

●

−2

−1

0

1

2

mice

islet expression

transcripts

29

E vs E

mice

expression in islet

transcripts

expression in liver

liver expression

transcript 512831 ● ● ● ●● ●●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ● ● ●●● ●● ●

1.0 0.5 0.0

−0.5 −1.0 −1.5

● ● ● ●

●

●

●

● ●

● ●● ● ● ●

● ● ● ●● ● ●● ● ●●● ●● ● ●● ● ● ● ●● ●● ● ● ● ● ● ●●●● ● ●● ● ●● ● ● ● ●●●● ● ● ● ●● ●● ● ● ● ●● ●● ● ●● ● ● ● ● ● ●● ● ● ● ● ●●● ● ●● ● ●● ●● ● ●●● ● ●● ● ● ●●●● ● ● ● ●●●● ● ●●● ●●● ● ● ●●●●● ● ● ● ● ●●● ●●●● ●● ●● ● ●●● ● ● ● ● ● ●● ● ● ●● ● ● ● ●● ● ●●● ● ●● ● ● ●● ●●●●● ● ● ● ●● ● ● ● ●

−1.0

● ● ●

● ● ● ● ●●

●

●

●

−0.5

0.0

0.5

1.0

mice

islet expression

transcripts

30

E vs E

mice

expression in islet

transcripts

expression in liver

liver expression

transcript 507042 1 ●

−2

●

●

● ●

−1

●

●

0

● ●● ● ●●● ● ●● ● ●●●●●●●● ●●●● ●●● ●● ● ● ● ●● ●● ● ● ● ●● ●● ● ● ●●● ●● ● ● ●●● ● ● ●● ● ● ● ●● ● ●● ● ● ●● ●● ● ●● ● ● ● ● ●● ●● ●● ● ●●● ● ● ● ● ● ● ● ● ● ●● ● ●●● ● ● ●● ●● ● ● ● ●● ●● ● ●●● ● ● ● ●● ●● ●● ● ●● ● ● ●● ● ●● ● ●● ● ● ● ● ●● ● ●● ● ●●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ●● ●● ● ●●● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●●●● ●●● ● ●● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●●● ●●● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ●● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ●

● ● ●● ● ● ● ● ● ● ●● ●●● ● ●●● ●● ● ● ● ● ●● ● ●● ●● ● ●●●● ● ● ● ●●● ● ● ● ● ●● ● ● ● ● ●● ●● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ●●● ●● ● ● ●● ● ●● ●●● ● ●●● ● ●●●● ● ● ●

● ● ●

●

−2.0

−1.5

−1.0

−0.5

0.0

0.5

1.0

mice

islet expression

transcripts

31

E vs E

mice

expression in islet

transcripts

mice

expression in liver

transcripts

32

E vs E

mice

expression in islet

Mouse3280 transcripts

expression in liver

liver expression

3

●

● ● ● ●● ● ● ● ● ●● ●● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ●● ● ●● ● ● ●

●

1 0

● ●

●

● ●

● ● ●● ●

−2

●

●

●

−1

−3

●

●

2

● ●● ● ● ●● ●

● ●

●

● ●

● ● ●

−1.5

−1.0

−0.5

0.0

0.5

1.0

1.5

mice

islet expression

transcripts

33

E vs E

mice

expression in islet

Mouse3598 ● ●

transcripts

expression in liver

liver expression

●

● ●

●

●

●

● ● ●

●

●

● ● ●● ● ● ● ●

● ● ●

●

●● ●

●

● ●

●

●

●

●

●

● ●●

● ●

●

0

●

● ●

●

1

● ●

● ● ● ● ● ● ● ● ●● ● ● ●

●

●

−1

●

●

●

●

●

● ● ●● ● ●

●

−2

●

●●

●

●

●

●

−2.0

−1.5

−1.0

−0.5

0.0

0.5

1.0

1.5

mice

islet expression

transcripts

34

E vs E

mice

expression in islet

transcripts

expression in liver

Mouse3599 liver expr

Mouse3599 liver vs Mouse3598 islet ●

2

● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ●● ●● ● ●● ● ● ● ● ●● ● ● ●● ● ●

1

●

0

● ● ●

● ●

−1

● ● ●

●

●

●●

● ●

● ●

−2

●● ● ●

●

●

●

●

●

●

● ● ● ●

●

● ● ●

● ●

● ●

● ● ●

−2.0

−1.5

−1.0

−0.5

0.0

0.5

1.0

1.5

mice

Mouse3598 islet expr

transcripts

35

E vs E

mice

expression in islet

transcripts

expression in liver

Mouse3598 liver expr

Mouse3598 liver vs Mouse3599 islet 1

●● ● ●

●

0

● ●●

●

● ● ● ●

−2

●

●

● ●

●

●

● ●

●

●

●

● ●

●

●

●

● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ●●● ● ● ● ● ● ● ● ● ● ● ●

●

●

●

−1

● ● ●● ●●

● ●●

●

● ●

●

●

−2.0

−1.5

−1.0

−0.5

0.0

0.5

1.0

1.5

mice

Mouse3599 islet expr

transcripts

36

E vs E −2

−1

0

1

−2 −1

0

1

2 1.5 1.0 0.5

Mouse3598 islet

−0.28

0.84

−0.24

0.0 −0.5 −1.0 −1.5 −2.0

●

●

● ● ● ● ●● ● ● ● ● ● ●● ●●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ●● ● ●● ● ●●● ●● ●●●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ●

Mouse3598 liver

● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ●● ● ●●● ● ●● ● ● ● ● ●●● ● ● ● ●● ● ● ●● ● ● ● ● ● ●● ● ● ● ●● ● ●● ●● ● ●● ● ● ● ● ● ●● ● ● ● ● ●● ●● ● ● ● ●

● ● ● ● ● ●● ● ● ● ● ●● ● ●● ● ● ● ●● ●●● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ●●● ● ●● ● ● ● ●●●● ● ● ● ●● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ●● ●

●

●

1 0 −1 −2

●

1 0 −1 −2

●

● ● ● ●●● ● ●● ● ● ● ●●● ● ●● ●● ● ● ●● ● ●●● ● ● ● ● ● ● ●● ● ● ●●●

● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ●● ● ●

−2.0

−1.0

●

1.0

Mouse3599 islet

● ● ● ● ●● ●●● ● ● ●

● ● ● ● ●● ●● ●● ● ● ●●● ●● ●● ● ●●●●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ●● ● ● ●●● ● ● ● ● ● ● ●

●●

●

0.0

−0.24

●

●

●

2

0.87

−0.27

1.5 1.0 0.5 0.0 −0.5 −1.0 −1.5 −2.0

● ● ● ● ●● ● ● ● ● ● ●●● ● ● ● ● ●●● ● ● ● ● ● ●● ●●● ● ●● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ●● ● ●● ● ● ● ● ● ●● ● ● ● ●●

●

●

−2.0 −1.0

0.0

Mouse3599 liver

●

1.0

37

E vs E −3

−1 0

Mouse3280 islet 3 2 1 0 −1 −2 −3

−1.5

−0.5

0.5

−0.18

−0.15

Mouse3280 liver

−0.29

−0.09

1.5 1.0 0.5 0.0 −0.5 −1.0 −1.5

● ● ● ● ● ●● ● ●●● ● ●● ● ●● ● ● ● ●●● ●●● ●● ● ●● ●● ● ● ●● ● ● ● ● ● ● ●●● ● ● ● ● ● ●●● ●● ● ● ● ●● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ●

● ●

●

● ● ● ●● ● ● ● ● ● ●● ●

●●

● ● ● ● ● ●●● ● ● ●●● ● ●●● ● ● ● ● ● ● ● ●● ● ●● ● ●●● ● ● ●●●● ●● ● ● ●● ●● ● ● ●● ● ● ● ● ● ●● ●

●

●

●

0.5

● ● ● ●● ● ●

0.0

●

● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ●●●● ● ●● ● ●● ● ● ● ● ● ● ● ●●● ● ● ●●● ● ● ● ● ● ●● ●

● ●

● ● ● ● ● ●● ● ● ● ● ● ●

−1.5 −0.5

0.5

1.5

●

1.0 ●

●

0.5

Mouse3281 islet

0.85

●

0.0 −0.5 −1.0

● ● ●● ● ●● ● ●●● ●

−1.5 −2.0

●

● ●● ● ● ●●

−0.5 −1.5

3

0.80

●

−1.0

2

●

● ●● ● ● ●● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ●● ●●● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ●● ● ●

1.0

1

● ● ● ●● ● ● ●● ● ● ● ● ●● ● ●● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ●● ●●● ● ● ● ● ● ●● ● ●● ●● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ●● ● ●

●● ●● ●●● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ●●●● ● ●● ● ● ● ● ● ●● ● ● ● ●●●● ●● ● ● ●● ● ● ● ●

●

● ● ●

Mouse3281 liver

● ● ●●● ● ● ● ● ● ● ● ●

−2.0

−1.0

0.0

1.0

38

E vs E −2

−1

0

1

2

−1

0

1

2

1

Mouse3295 islet

0.90

0.97

0.37

0 −1 −2 −3

2

●●● ● ● ● ● ● ●● ●●● ● ●● ● ● ● ●●● ● ●● ●● ● ● ● ● ●● ●● ● ●● ● ● ● ● ● ●● ● ● ●● ● ● ●● ● ●

1 0 −1 ●

−2

●

●● ●● ●● ● ● ●● ● ●● ● ● ● ●● ● ● ● ●

●

● ● ●● ● ●● ●● ●●● ● ●●● ●●● ● ●●

●● ●● ● ●● ●●● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ●● ● ●● ● ● ● ● ● ●● ●●● ●● ●

●

Mouse3295 liver ● ● ●● ● ● ●● ●● ● ● ● ●● ● ●● ●● ●●● ● ● ● ● ● ● ● ● ● ●●● ●● ●● ●●● ●●●● ● ● ● ● ●● ● ● ● ●

● ● ● ● ●● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ●●

−1 ●

−3

● ● ● ●●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●●● ●● ●● ● ● ● ● ●●● ●● ● ● ● ● ●● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●

−2

1

Mouse3296 islet

0

0.43

−1

0

1

−1 −2 −3

●

0

0.35

●

2 1

0.88

● ● ● ● ●●● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ●●●● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ●● ● ●● ● ● ● ●● ● ● ● ● ● ●●

●

● ●

● ● ●● ● ● ● ●● ● ● ●

●

● ● ● ●● ● ● ●● ●● ●● ● ● ● ● ● ●● ● ● ● ●● ● ● ●● ●● ● ● ● ● ● ● ● ● ●● ●● ●● ● ● ● ● ●● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ●

−3 −2 −1

0

Mouse3296 liver

1

39

Expression mix-ups adipose 3583 ●

islet ● 3584 ● 3295 ●

● 3296

3598 ●

● 3599

● 3187 3200 ●

● 3188

gastroc

kidney ● 3484 ●

3655 ●

?

● 3503 ●

● 3659 3510 ●

hypo 3179 ●

● 3188

3208 ●

● 3210

3347 ●

● 3348

3367 ●

● 3369

3381 ●

● 3382

● 3523

liver

3449 ●

● 3451

3452 ●

● 3454

3589 ●

● 3590

3592 ●

● 3594

● 3136 ●

● 3141

3142 ●

● 3143

40

Insulin QTL after before

8

LOD score

6

4

2

0 1

2

3

4

5

6

7

8

9

10

11

12 13

14 15 16 17 18 19

X

Chromosome

41

Strong eQTL probe 499541 (on chr 1)

400

LOD score

300

probe 10002916257 (on chr 13) 200

100

0 1

2

3

4

5

6

7

8

9

10

11

12 13

14 15 16 17 18 19

X

Chromosome

42

Summary ▶

Sample mix-ups happen

▶

With eQTL data, we can both identify and correct mix-ups

▶

There is great value in having expression on multiple tissues

▶

The general idea here has wide application for high-throughput data

▶

Broman et al. (2015) G3 5:2177-2186 doi: 10.1534/g3.115.019778

▶

Related work: – Westra et al. (2011) Bioinformatics 27:2104–2111 – Schadt et al. (2012) Nat Genet 44:603–608 – Ekstrøm and Feenstra (2012) Stat Appl Genet Mol Biol 3:Article 13 – Lynch et al. (2012) PLoS ONE 7:e41815 43

Lessons ▶

Don’t fully trust anyone – Including yourself

▶

Make lots of plots – Don’t rely on summary statistics, like LOD scores – Look at responses on the original scale

▶

Follow up all aberrations

▶

Take your time with data cleaning – A month, two months, a year?

▶

If you have big rectangles whose rows correspond, check that they actually correspond 44

E vs G

0.0

● ●●● ● ● ● ●● ● ● ● ●●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ●● ● ●●

Transformed 1.5

● ●

● ● ● ●● ● ●● ●

●

−0.5

−1.0

●● ●●

● ● ●● ● ●

●

●

●●

● ● ● ●● ● ●● ●●● ● ●● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ●

transformed expression of 499541

expression of 499541

Untransformed ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ●●● ●●● ● ● ● ● ● ●● ● ●●● ● ●

1.0 0.5 0.0

● ● ● ● ● ●● ●● ● ●● ●● ● ● ●●● ●● ● ● ● ●● ●● ● ●●● ●● ● ●● ● ● ●● ● ●● ● ● ●●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ●● ● ● ● ● ● ●● ● ● ●● ●

−0.5

●

●●

−1.0

●

● ● ●● ● ● ●● ● ● ●● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ●

−1.5

●

● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ●● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ●●● ●●● ●● ● ● ● ● ● ● ● ● ● ●● ●● ● ●●●● ●● ●●● ●● ●● ●● ● ● ● ●● ● ● ● ● ●

−2.0 BB

BR

RR

Genotype at rs13476158

BB

BR

RR

Genotype at rs13476158

45

Lessons ▶

Don’t fully trust anyone – Including yourself

▶

Make lots of plots – Don’t rely on summary statistics, like LOD scores – Look at responses on the original scale

▶

Follow up all aberrations

▶

Take your time with data cleaning – A month, two months, a year?

▶

If you have big rectangles whose rows correspond, check that they actually correspond 46

Acknowledgments Alan Attie Mark Keller

Biochemistry, UW–Madison

Brian Yandell

Statistics and Horticulture, UW–Madison

Christina Kendziorski Aimee Teo Broman

Biostat & Medical Info, UW–Madison

Eric Schadt

Mount Sinai

Danielle Greenawalt Amit Kulkarni

Merck & Co., Inc.

Śaunak Sen

UT-Memphis

NIH: R01 GM074244, R01 DK066369

47

Slides: bit.ly/berkeley2017 kbroman.org github.com/kbroman @kwbroman

48

Decisions Self vs best 0.8

self−self distance

0.6

Next−best vs best

Fixable

● ●● ● ●● ● ● ● ● ● ● ●● ● ●● ● ● ●● ● ● ●● ●●● ● ●● ●● ● ● ● ● ● ● ● ● ●● ●●● ●● ●● ● ● ● ● ● ●● ● ● ● ● ●●● ●●●● ● ●

0.8

Not found ●

● ● ●

● ● ●

2nd smallest distance

●

●● ●

● ●

0.4

0.2

0.6

0.4

0.2

●

● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ●● ●●● ● ●●● ● ● ●

● ●

● ●● ● ●● ● ● ● ● ● ●●

●

● ●

●

0.0

● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

0.0

Good 0.0 0.2

0.4

0.6

minimum distance

0.8

0.0

0.2

0.4

0.6

0.8

minimum distance

49