gene identification 2015 · comparative genomics approach comparative genomics identifies a...
TRANSCRIPT
![Page 1: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/1.jpg)
GENE IDENTIFICATION Bruce R. Korf, M.D., Ph.D. Department of Genetics
![Page 2: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/2.jpg)
GENE DISCOVERY
http://www.genome.gov/Pages/News/PaceofDiseaseGeneDiscovery.pdf
![Page 3: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/3.jpg)
POSITIONAL CLONING
![Page 4: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/4.jpg)
LINKAGE
![Page 5: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/5.jpg)
INDEPENDENT ASSORTMENT
![Page 6: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/6.jpg)
“COMPLETE” LINKAGE
![Page 7: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/7.jpg)
10% RECOMBINATION
![Page 8: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/8.jpg)
LIKELIHOOD RATIO
![Page 9: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/9.jpg)
LINKAGE ANALYSIS
![Page 10: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/10.jpg)
LINKAGE DISEQUILIBRIUM
A
A
A
a
a
a
B
B
B
B
B
B
A
A
A
a
a
a
B
B
B
B
b
B
![Page 11: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/11.jpg)
HAPLOTYPE ANALYSIS
![Page 12: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/12.jpg)
![Page 13: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/13.jpg)
HUMAN GENOME
Repeated and non-coding sequences Coding
sequences
• Non-coding RNAs • tRNA • rRNA • snRNA • other non-coding RNAs
• Protein-encoding RNAs
• Interspersed repeats (LINE/SINE) • Pseudogenes • Simple sequence repeats • Segmental duplications • Highly repeated sequences
Human Genome: 3.15 billion base pairs
![Page 14: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/14.jpg)
GENOME BROWSER
http://genome.ucsc.edu
![Page 15: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/15.jpg)
Nature Genetics 36, 400 - 404 (2004) Mutations in VPS33B, encoding a regulator of SNARE-dependent
membrane fusion, cause arthrogryposis–renal dysfunction–cholestasis (ARC) syndrome Paul Gissen, et al.
Nature Genetics 36, 400 - 404 (2004)
![Page 16: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/16.jpg)
CANDIDATE GENES
Nature Genetics 36, 400 - 404 (2004)
![Page 17: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/17.jpg)
INTEGRATIVE GENOMICS
Proc. Natl. Acad. Sci. USA, Vol. 100, Issue 2, 605-610, January 21, 2003
![Page 18: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/18.jpg)
MAPPING, GENOMICS, PROTEOMICS
Proc. Natl. Acad. Sci. USA, Vol. 100, Issue 2, 605-610, January 21, 2003
![Page 19: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/19.jpg)
LRPPRC MUTATIONS IN LEIGH DISEASE
Proc. Natl. Acad. Sci. USA, Vol. 100, Issue 2, 605-610, January 21, 2003
![Page 20: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/20.jpg)
COMPARATIVE GENOMICS APPROACH
Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene
Jin Billy Li1, Jantje M. Gerdes2, Courtney J. Haycraft4, Yanli Fan5, Tanya M. Teslovich2, Helen May-Simera6, Haitao Li7, Oliver E. Blacque5, Linya Li1, Carmen C. Leitch2, Richard Allan Lewis8, Jane S. Green9, Patrick S. Parfrey9, Michel R. Leroux5, William S. Davidson5, Philip L. Beales6, Lisa
M. Guay-Woodford7, Bradley K. Yoder4, Gary D. Stormo1, Nicholas Katsanis2, 3 and Susan K. Dutcher
Cell 117, Issue 4 , 14 May 2004, Pages 541-552
![Page 21: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/21.jpg)
PROTEINS FOUND IN HUMAN AND CHLAMYDOMOMAS BUT NOT ARABIDOPSIS
(FLAGELLAR PROTEINS)
![Page 22: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/22.jpg)
BARDET-BIEDL SYNDROME • Obesity
• Polydactyly
• Retinitis pigmentosum
• Renal failure
• Genetic heterogeneity
• Some forms associated with genes involved in cilia http://www.emedicine.com/oph/
images/199OPH0704-04.jpg
www.makeachildsmile.org/ 2003/
prev_2003_dec.shtml
![Page 23: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/23.jpg)
BBS5
2 proteins in database map to 2q31 where BBS5 known to map
![Page 24: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/24.jpg)
IMMOBILIZATION/AMPLIFICATION
Metzker, M. Nature Reviews Genetics 2010;11:3146.
![Page 25: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/25.jpg)
DNA SYNTHESIS/DETECTION
Metzker, M. Nature Reviews Genetics 2010;11:3146.
![Page 26: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/26.jpg)
EXOME SEQUENCING
Bamshad et al. Nat. Rev. Genet. 2011; 12:745.
AGGTCGTTACGTACGCTACGACCTACATCAGTACATAGGCATGACAAAGCTAGGTGT
![Page 27: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/27.jpg)
NUMBER OF VARIANTS
Bamshad et al. Nat. Rev. Genet. 2011; 12:745.
g
Variant type Mean number of variants (± sd) in African Americans
Mean number of variants (± sd) in European Americans
Novel variants
Missense 303 (± 32) 192 (± 21)
Nonsense 5 (± 2) 5 (± 2)
Synonymous 209 (± 26) 109 (± 16)
Splice 2 (± 1) 2 (± 1)
Total 520 (± 53) 307 (± 33)
Non-novel variants
Missense 10,828 (± 342) 9,319 (± 233)
Nonsense 98 (± 8) 89 (± 6)
Synonymous 12,567 (± 416) 10,536 (± 280)
Splice 36 (± 4) 32 (± 3)
Total 23,529 (± 751) 19,976 (± 505)
Total variants
Missense 11,131 (± 364) 9,511 (± 244)
Nonsense 103(± 8) 93 (± 6)
Synonymous 12,776 (± 434) 10,645 (± 286)
Splice 38 (± 5) 34 (± 4)
Total 24,049 (± 791) 20,283 (± 523)
![Page 28: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/28.jpg)
STRATEGIES
Bamshad et al. Nat. Rev. Genet. 2011; 12:745.
![Page 29: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/29.jpg)
Nature Genetics 2010;42:30-35.
Miller syndrome
![Page 30: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/30.jpg)
EXOME SEQUENCING
Nature Genetics 2010;42:30-35.
![Page 31: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/31.jpg)
COMMON DISEASE – COMMON VARIANT
HYPOTHESIS Common diseases accounted for by genetic variants
found in 1-5% of population
Linkage disequilibrium
![Page 32: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/32.jpg)
SNP ASSOCIATION
Hypothesis: Allele 2 is associated with an increased risk of asthma
ACTAGGA
ACTCGGA
Allele 1
Allele 2 Asthma" No Asthma"
Allele 2 Present" 30" 10"
Allele 2 Not Present"
70" 90"
![Page 33: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/33.jpg)
ASSOCIATION ANALYSIS
![Page 34: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/34.jpg)
Recombination hot spot
SNP
![Page 35: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/35.jpg)
Klein et al., Science (80- ). 2005 April 15; 308(5720): 385–389.
Complement Factor H Polymorphism in Age-Related Macular Degeneration
http://www.medrounds.org/amd/uploaded_images/fig2-757825.JPG
![Page 36: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/36.jpg)
ASSOCIATIONS FOR T2D Gene" Symbol"
Cyclin-dependent kinase inhibitor 2" CDKN2A/B"
Insulin-like growth factor 2 mRNA binding protein" IGF2BP2"
CDK5 regulatory subunit associated protein 1-like 1" CDKAL1"
Hematopoietically-expressed homeobox" HHEX"
S35-like splicing factor 30" SCL30A8"
Transcription factor 7-like 2" TCF7L2"
FATSO" FTO"
Peroxisome proliferator-activated receptor gamma" PPARG"
Potassium channel inwardly rectifying, subfamily J, member 11" KCNJ11"
![Page 37: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/37.jpg)
MISSING HERITABILITY
Manolio et al. Nature 461:747, 2009
![Page 38: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/38.jpg)
38
![Page 39: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/39.jpg)
RELATIVE RISK Asthma" No Asthma"
Allele 2 Present" 30" 10"
Allele 2 Not Present"
70" 90"
Risk of asthma in allele 2 carrier = 30/40 = 0.75 Risk of asthma in non allele 2 carrier = 70/160 = 0.4375
Relative risk = 0.75/0.4375 = 1.71
![Page 40: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/40.jpg)
ODDS RATIO Asthma" No Asthma"
Allele 2 Present" 30" 10"
Allele 2 Not Present"
70" 90"
Odds: ratio of probability event will happen over probability event will not happen – e.g., allele carrier getting asthma or not getting asthma
![Page 41: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/41.jpg)
RELATIVE RISK VS. ODDS RATIO
Asthma" No Asthma"
Allele 2 Present" 30 = a" 10 = b"
Allele 2 Not Present"
70 = c" 90 = d"
![Page 42: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/42.jpg)
ODDS VS. ABSOLUTE RISK OF DISEASE
= 3.5/1000 2.3/1000
52% increase in odds = 1.52
![Page 43: Gene Identification 2015 · COMPARATIVE GENOMICS APPROACH Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene Jin Billy Li1,](https://reader036.vdocuments.net/reader036/viewer/2022081614/5fc165e80d248b28bc1725ea/html5/thumbnails/43.jpg)
CALCULATION OF RISK
Risk = (Population risk)(odds ratio)
Example: Population risk is 3.5%
Odds ratio is 1.2 Risk = (3.5)(1.2) = 4.2%