1. Genetic Variations Resources May 15, 2013 Ansuman Chattopadhyay, PhD, Head Molecular Biology Information Service Health Sciences Library System University of Pittsburgh ansuman@pitt.edu http://www.hsls.pitt.edu/guides/genetics

2. Objective  Human genetic variations  Genetic variations databases  Functional analysis of mutations/SNPs

3. Topics  Databases:  dbSNP  db GAP  GenPheni  DGV  Decipher  OMIM  HGMD  Regulome db  Tools  HugeNavigator  FastSNP  SPOT  GenomeTrax

4. Human Genetic Variations 1bp 1kb 1Mb >5Mb Duplications Deletions Insertions

5. Human Genome Variations 321,340,1 bp (0.11 % of the genome) : SNPs 40,568,593 bp (1.35% of the genome) : CNVs Scherer, S.W. (2009), "Copy number variation", in Scherer, S. (ed.), Copy Number Variation:, The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London

7. SNP Facts

8. Life Cycle of SNPs and Mutations Mutation/ Private SNP SNPs

10. Classifications of SNPs Genomic location based

11. Classifications of SNPs Nucleotide substitution based

12. Polymorphisms and Disease Markers

13. International Hap Map Project http://www.hapmap.org/  Whole-genome genotyping of 10 million SNPs  Technologically daunting  Prohibitively expensive  Researchers tried to downsize the problem of genome-wide genotyping by studying haplotypes.  A haplotype is a contiguous, linear set of SNP alleles along a genome that is inherited as a block.

14. The Origin of Haplotype

15. Haplotype Blocks

16. Haplotype and Tag SNPs

17. Hap Map Population

19. http://www.1000genomes.org/about

22. Bioinformatics Institutions http://www.ebi.ac.uk/ http://www.ncbi.nlm.nih.gov/

23. dbSNP

24. dbSNP Stats as of January 25, 2010 http://www.ncbi.nlm.nih.gov/SNP/snp_summary.cgi

25. Current Status of dbSNP MassGenomics blog by Dan Koboldt http://goo.gl/TwltA

26. dbSNP Data Types

27. Ref SNP : rs4244285

29. Genetic Terminologies

30. Ref SNP : rs4244285

31. Submitted SNP: ss5586415

32. SNPedia and NextBio http://goo.gl/aOsoX http://goo.gl/Lqqd4

33. Searching dbSNP  Identify  SNPs present in a gene sequence  SNPs reported to be present in a genomic region

34. Searching dbSNP UCSC Genome Browser UCSC Table Browser NCBI dbSNP page http://www.ncbi.nlm.nih.gov/snp

35. Searching dbSNP

37. dbSNP Search result Display

38. GWAS

39. GWAS Plot Each SNP is assessed for ‘‘genome-wide’’ significance, after Bonferroni correction.

40. Publications on HapMap Hap map GWAS

41. Genome Wide Association Studies http://www.genome.gov/gwastudies/

42. Find SNPs for a Disease/Trait CDC developed HuGENavigator : http://hugenavigator.net/http://hugenavigator.net/

43. GWAS Integrator

44. What SNPs are associated with “asthma”?

45. GWAS Integrator : rs7216389rs7216389

46. GWAS Integrator What SNPs are associated with “asthma”?

47. GWAS Integrator

48. GWAS Integrator : rs7216389rs7216389 Ref: Moffatt Mf etal. childhood asthma. Nature. 2007 Jul 26;448(7152):470-3. Epub 2007 Jul 4. PubMed PMID: 17611496.

49. GWAS Integrator : rs7216389rs7216389

50. Find associated Genes for a Disease/Trait

51. Gene Prospector: Asthma

53. HuGE Navigator An integrated, searchable knowledge base of genetic associations and human genome epidemiology

54. PheGenI

55. Clinically Associated Mutations OMIM HGMD

56. Online Mendelian Inheritance in Man (OMIM)

57. OMIM

60. Epigenome and Encyclopedia of DNA Elements Project

61. Spatiotemporal gene expression TP53 EGFR

62. A movie on regulated transcription http://vcell.ndsu.edu/animations/regulatedtranscription/index.htm

63. Epigenetic mechanisms Source: NCBI http://www.ncbi.nlm.nih.gov/books/NBK45788/#epi_sci_bkgrd.About_Epigenetics

64. Genome in 3D http://www.nature.com/nature/journal/v470/n7333/pdf/470289a.pdf

65. Chromatin Immuno-Precititation-Seq (ChIP-Seq)

66. Epigenetic Markers Landmark Paper : http://www.nature.com/ng/journal/v39/n3/full/ng1966.html

67. Histone Modifications http://goo.gl/GQ9V8 http://www.hsls.pitt.edu/guides/genetics

68. Encode Project http://www.genome.gov/10005107

69. http://goo.gl/QeIbQ

71. Regulome

72. Regulome db Search rs7216389 rs2853669

74. Hands-on Exercise on Searching dbSNP  Mutations in the human BRCA1 gene are reported to be associated with the early onset of breast cancer.  How many coding nonsynonimous SNPs have been reported to be associated with this gene?  How many of these SNPs shows >40% heterozygosity?  Pick a SNP from the list and find the position of its protein sequence, which shows aa change due to this SNP.  How many in dels are reported to be present in the chromosome chr21: region 33,031,597-33,041,570 ?

75. Hands –On Exercise Identify genes and SNPs associated with your disease/trait of interest Crohn’s disease, Prostate cancer, LDL cholesterol

77. Structural Variations ABC ABCBB ABC AC ADCB Normal Duplication Inversion Deletion Insertion CNV

78. Structural Variations

79. Structural Variations Databases Database of Genome Variations (DGV) dbVar DECIPHER dbRIP Mitelman Breakpoint Database

80. DGV

81. DGV :Genome wide view

82. DGV

83. DGV: Chr 1

84. DGV

85. Hands-on Exercise Is the CETN1 or Grip1 gene located in a region that is copy number variable? Are there any other genes in this region? Can you find any Inversions or In Dels there as well? What is the frequency of the CNV reported in the study population?

86. DGV Genome Browser

87. DGV: Genome Browser

88. dbVar

89. DECIPHER https://decipher.sanger.ac.uk/application/dashboard

90. DECIPHER Syndrome Report

92. Structural Variations Databases Genome Variation Database (DGV) dbVar DECIPHER dbRIP Mitelman Breakpoint Database

93. dbRIP http://dbrip.brocku.ca/searchRIP.html

94. Mitelman Breakpoint

95. Hands-On Exercise Generate an integrated variation map with reference SNPs, Mitelman breakpoints and OMIM diseases for chromosome 17; region 7773,000-7792,000 bp. What gene(s) have you found in this region? Answer key: http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Variation/Exercises/var_qa3.html http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Variation/Exercises/var_qa3.html

96. Map Viewer Setup http://www.ncbi.nlm.nih.gov/projects/mapview

97. Map Viewer Setup

98. Genetic Variations Map

99. Online Mendelian Inheritance in Man (OMIM)

100. OMIM

101. UCSC Table Browser

102. Hands-on Exercise Find all human genes which have only one exon. How many of these also show CNVs? Tips: Use UCSC Table Browser

103. Biobase Genome Trax and HGMD http://goo.gl/pUhQ4

104. Variant File : VCF

105. GenomeTrax Input

106. GenomeTrax Result

108. Functional Analysis of SNPs http://www.hsls.pitt.edu/guides/genetics

109. SNPs and the Structure of a Gene http://www.hsls.pitt.edu/guides/genetics

110. Decision Tree for SNP Analysis http://www.hsls.pitt.edu/guides/genetics

111. Exonic Splicing Enhancer/Silencer http://www.hsls.pitt.edu/guides/genetics

112. Functional Analysis of SNPs A gene variant primarily found in African Americans, that slightly increases the risk for developing an irregular heartbeat, known as arrhythmia. The variant occurs in the cardiac sodium channel gene SCN5A which results a change of amino acid at the position of 1102 from serine to tyrosine (S To Y). Can you predict the effect of this non-synonymous SNP (rs7626962). Answer http://www.hsls.pitt.edu/guides/genetics

113. Functional Analysis of SNPs

114.  Entrez SNP - Search Entrez SNP by refSNP ID to find SNP information. Entrez SNP  Entrez Protein - Find protein information including its amino acid sequence and the presence of functional domains Entrez Protein  NCBI Amino Acid Explorer - Compare amino acids in terms of physyo-chemical properties NCBI Amino Acid Explorer  NCBI Mutation Analyzer - Predict the effect of amino acid change on the protein structure NCBI Mutation Analyzer  TMHMM Server v. 2.0 - Predict the presence of transmembrane helix in a protein sequence TMHMM Server v. 2.0  Russel etal., Amino Acid Properties Table - Predict the effect of amino acid change on the protein structure Russel etal., Amino Acid Properties Table

115. SNP Gene View for SCN5A

116. Multiple Sequence Alignment http://www.hsls.pitt.edu/guides/genetics

117. Amino Acids Comparison NCBI Amino Acid Explorer http://www.hsls.pitt.edu/guides/genetics

118. Compare Amino Acids Properties Amino Acid Properties Table: http://www.russell.embl.de/aas/ http://www.russell.embl.de/aas/ http://www.hsls.pitt.edu/guides/genetics

119. Amino Acids Substitution Preference http://www.hsls.pitt.edu/guides/genetics

120. Tools for Amino Acid Substitution Effect Prediction SIFT  http://sift.jcvi.org/ http://sift.jcvi.org/ PolyPhen  http://genetics.bwh.harvard.edu/pph/ http://genetics.bwh.harvard.edu/pph/ SNPs3D  http://www.snps3d.org/ http://www.snps3d.org/ pMUT  http://mmb2.pcb.ub.es:8080/PMut/ http://mmb2.pcb.ub.es:8080/PMut/ http://www.hsls.pitt.edu/guides/genetics

121. Comparison of AAS prediction tools Pauline C. Ng and Steven Henikoff, Annu. Rev. Genomics Hum. Genet. 2006. 7:61–80

122. Tools on Functional SNP Analysis Search.HSLS MolBio link http://search.hsls.pitt.edu/vivisimo/cgi-bin/query- meta?v%3aproject=BioInfoTools&v%3afile=viv_B7AUre&v%3aframe=list&v%3astate=root%7cN891&id=N891&act ion=list& http://search.hsls.pitt.edu/vivisimo/cgi-bin/query- meta?v%3aproject=BioInfoTools&v%3afile=viv_B7AUre&v%3aframe=list&v%3astate=root%7cN891&id=N891&act ion=list& FASTSNP -- an always up-to-date and extendable service for SNP function analysis and prioritization http://fastsnp.ibms.sinica.edu.tw/ F-SNP: computationally predicted functional SNPs for disease association studies. http://compbio.cs.queensu.ca/F-SNP/ http://www.hsls.pitt.edu/guides/genetics

123. FASTSNP Analysis http://www.hsls.pitt.edu/guides/genetics

124. FASTSNP Analysis http://www.hsls.pitt.edu/guides/genetics

125. F-SNP : A Collection of Functional SNPs Specifically Prioritized for Disease Association studies http://www.hsls.pitt.edu/guides/genetics

126. F-SNP : A Collection of Functional SNPs Specifically Prioritized for Disease Association Studies http://www.hsls.pitt.edu/guides/genetics

127. Tutorials and References Advanced Course on NCBI Resources (Browser: IE, select.html format) Predictive Functional Analysis of Polymorphisms: An Overview Predictive Functional Analysis of Polymorphisms: An Overview Authors:Michael R. Barnes Book:Bioinformatics for Geneticists Source:Wiley InterScience: Online Books Functional In Silico Analysis of Non-Coding SNPs Authors:Thomas Werner Book:Bioinformatics for Geneticists Source:Wiley InterScience: Online Books Predicting the Effects of Amino Acid Substitutions on Protein Function Predicting the Effects of Amino Acid Substitutions on Protein Function  Pauline C. Ng and Steven Henikoff  Fred Hutchinson Cancer Research Center, Seattle,Washington 98109;

128. Thank you! Any questions? Carrie IwemaAnsuman Chattopadhyay iwema@pitt.eduansuman@pitt.edu 412-383-6887412-648-1297 http://www.hsls.pitt.edu/guides/genetics