lobSTR: A Short Tandem Repeat Profiler for Personal Genomes - PowerPoint Presentation

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lobSTR:

A Short Tandem Repeat Profiler for Personal Genomes

CSE291

02/16/17

Melissa Gymrek

02/16/17

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

We know quite a lot about genetic variation…

Huntington

Fragile X

OPMD

Synpolydactyly

Ataxia (10 types)

HFG syndrome

Holoprosen-cephaly

Pseudoach-ondroplasia

Myotonic

dystrophy

Cleidocranial

DysplasiaALS-FTD

STRs – domains of interest

Despite multitude of applications, STRs are not routinely profiled in whole genome sequencing

1. Medical genetics - more than 40 documented diseases2. Forensics – 12 million STR profiles

3. Genetic genealogy – a vantage point to recent events.

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

ATGT

CAGCAGCAGCAGCAGCAG

CTGA

02/16/17

Challenges in profiling STRs from short reads

1. Only reads entirely spanning an STR are informative

[

C

AA

]

5

Ambiguity

TGACGCATGATGT

C

AA

C

AA

C

AA

C

AA

Non informative read:

[

C

AA

]

4

:

:

[

C

AA

]

??

ATGT

C

AA

C

AA

C

AA

C

AA

C

AA

C

AA

CTGA

Informative read:

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17

2. Non-reference alleles present as large indels

ATGT

C

AA

C

AA

C

AA

C

AA

C

AA

C

AACAACAAC

AACAACAATTGAGenome of interest:Reference:ATGTCAACAA

CAACAACAACAATTGA15bp indel

Challenges in profiling STRs from short reads

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17

Challenges in profiling STRs from short reads

3. PCR

“stutter noise” complicates calling

Capillary electrophoresis

ATGT

C

AA

C

AA

C

AA

C

AA

C

AA

CAATTGAATGTCAACAACAACAA

CAA

CAATTGA

ATGT

C

AA

C

AA

C

AA

C

AA

C

AA

C

AA

TTGA

ATGT

C

AA

C

AA

C

AA

C

AA

C

AA

***

TTGA

ATGT

C

AA

C

AA

C

AA

C

AA

C

AA

***

TTGA

ATGT

C

AA

C

AA

C

AA

CAA******TTGASequence reads

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17

lobSTR algorithm

lobSTR: an end-to-end solution for STR-profiling

Takes FASTA/FASTQ/

BAM and outputs VCF

Reports read alignments and STR alleles

Supports multi-threading

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17

Aim

: Find informative reads

and

characterize

STR

Sensing

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17

Entropy score successfully detects STRs

S

j

: sequence

j

Σ

: symbol alphabet (

dinucleotides

)

f

i

:

frequency of symbol

i

98.3%99.4%

AGCATATATATATATATATATAT

G

i

f

i

AG

0.04

GC

0.04

CA

0.04

AT

0.43

TA

0.39

TG

0.04

…

…

E(S) = 1.8

i

f

i

A

0.46

C

0.04

G

0.08

T

0.42

E = 1.54

CAGCTATTCGGGACTGAGCGGTAT

i

f

i

A

0.21

C

0.21

G

0.33

T

0.25

E = 1.97

i

f

i

CA

0.04

AG

0.08

GC

0.08

TA

0.08

TT

0.04

TC

0.04

…

…

E(S) = 3.71

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17

Entropy score partitions reads

TTTTGTGTGAAACCATGCTCGA

GTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTG

GTGTCTTAAGACTGAAATATCTAAGATTAACTTGG

Left flank

Right flank

STR region

2/22/12

lobSTR

(TG)n

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17

Aim

: Map STRs to the genome

Alignment

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17

Avoid gapped alignment by aligning non-repetitive regions

TTTTGTGTGAAACCATGCTCGA

GTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTG

GTGTCTTAAGACTGAAATATCTAAGATTAACTTGG

Divide and conquer approach:

Build an index of all genomic STRs

Align only the flanking regions to the reference

genome

Use paired end information to add specificity

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17

Aim

: determine the STR alleles

Allelotyping

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17

Removing PCR stutter noise

Stutter probability primarily depends on STR period

Period (

bp

)

Probability of stutter

Train parameters on

hemizygous

loci (male sex

chroms

)

Most stutter events are +/-1 from true allele

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17

Determine the most likely allelotype

R = (13, 13, 13, 14, 14, 14, 15)

17,17

16,16

16,17

15,15

15,16

16,17

14,14

14,15

14,16

14,16

13,13

13,14

13,15

13,16

13,17

12,12

12,13

12,14

12,15

12,16

12,17

11,11

11,12

11,13

11,14

11,15

11,16

11,17

Grid search to find maximum likelihood allelotype

L(

reads|allelotype;model

)

Return confidence score:

L(ML allelotype)

Σ

L(allelotype)

Allele 1

Allele 2

17,17

16,16

16,17

15,15

15,16

16,17

14,14

14,15

14,16

14,16

13,13

13,14

13,15

13,16

13,17

12,12

12,13

12,14

12,15

12,16

12,17

11,11

11,12

11,13

11,14

11,15

11,16

11,17

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17

lobSTR outperforms mainstream short read aligners at STR loci

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17

And now…

HipSTR

!

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17

And now…

HipSTR

!

Melissa Gymrek

Profiling STR variation in humans

Intro.

lobSTR

STR Catalog

Conclusion

02/16/17