Molecular Polymorphism: Pharmaco-Toxicogenomic GNSA 510 (Part I) PDF

# Molecular Polymorphism: Pharmaco-Toxicogenomic GNSA 510 (part I) ## Outline * SNPs/ different types of Variations * Abundance * Classification: what they are -Type of SNP? alleles? CNVs/Indels/etc... * Distribution: where they are -genomic position and how they are distributed (intra...

# Molecular Polymorphism: Pharmaco-Toxicogenomic GNSA 510 (part I) ## Outline * SNPs/ different types of Variations * Abundance * Classification: what they are -Type of SNP? alleles? CNVs/Indels/etc... * Distribution: where they are -genomic position and how they are distributed (intra and inter-population) * LD and Haplotypes * Paper analysis * SNPs Application Technology * SNPs Detection Technique/ Genotyping * SNPs in Inherited Disease ## Insertion-Deletion INDEL INDEL insertion or deletion could cause a net gain or loss in nucleotides ### INDELS | Regions | Length of INDEL | Outcome | | ---------------- | ---------------- | --------------------------------------------------------------------- | | Coding regions | Multiple of 3 | Maintenance of the open reading frame of the protein | | | Not multiple of 3 | Frameshift mutation? Premature termination codons PTCS | | Non-coding regions | Multiple of 3 | In promoter regions can alter transcriptional activity | ## The first large-scale efforts to identify INDELs in the human genome were focused on human chromosome 22. 13% of the variants on this chromosome were INDEL polymorphisms. A diagram of human chromosome 22 shows different regions; cat eye, DGS/VCFS, as well as 11:22, 9:22, and 11:22 constitutional, ALL, and Ewing's ## Five major INDEL classes: * Insertions or deletions of simple base pairs * Monomeric base pair expansions * Multi-base pair expansions of 2-15 bp repeat units * Transposon insertions * INDELs containing random DNA sequences ranging from 2 to 9,989 bp in length ## Importance of INDELs * Alter human phenotypes and also cause human diseases * Used in forensic analysis * Used as genetic markers in natural populations, especially in phylogenetic studies These polymorphisms originate from single mutation effect and have low mutation rate advantages over STRs ## Mapping INDELs * Useful to integrate the map of human INDEL variation into the HapMap. * A more complete description of the variation that is carried in each haplotype block and would facilitate efforts to identify the specific variation. * Serve as genetic markers for the HapMap. * Comprehensive variation maps, which include both SNPs and INDELs, will be more effective than SNP maps alone for identifying variants. ## Identification: Short or long reading sequencing, aCGH/Exome sequencing, GWAS ## Detection of Insertions and Deletions, Including Deconvolution of Het-Indels in Sanger Resequencing Projects using Mutation Surveyor® Software ### Introduction Insertions and deletions (INDELS), also known as deletion and insertion polymorphisms (DIP) and deletion insertion variations (DIV), may create a new stop codon and terminate the amino acid translation, resulting in severe genetic diseases. Although Next Generation sequencing techniques have increased in popularity and proven to be useful, Sanger Sequencing remains the gold standard for genome sequencing projects. These large resequencing projects demand fully automated calls of the heterozygous indels in determining the disease causing mutations. Among the diseases caused by indels are Tay-Sachs disease, Alzheimer's disease, and various forms of cancer 23. Mutation Surveyor is a unique software package which detects both homozygous and heterozygous INDELS. To detect INDELS Mutation Surveyor uses a proprietary algorithm which compares the mobility of the sample trace to the reference trace, and when a change is noted gaps the reference or sample trace until realignment is possible. This technology has proven to detect INDELS with greater than 99% accuracy when bi-directional sequences of greater than Plured 20 are employed. ## Technologies to Identify Indels * Next-Generation Sequencing (NGSPCR-based methods) * FISH (Fluorescence In Situ Hybridization) * SV detection algorithms: Tools like GATK (Genome Analysis Toolkit), Delly, or Manta ## Definition of CNV | Property | Value | | ------------- | ----------------------------------------------- | | Origin | *Inherited, *De novo | | Range | *Single bp changes, *Multi mega base chr | | Frequency | *Rare, *Common | | Target Region | *Single gene, *Dozens of gene, *No genes | ## CNV types | Type | Description | | --------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Duplication | A segment of DNA is duplicated, resulting in an extra copy of the genes within that segment. This can lead to an increase in gene expression and potentially to phenotypic changes. | | Deletion | A segment of DNA is deleted, resulting in a loss of genes within that segment. This can lead to decreased gene expression and potentially to phenotypic changes. | | Translocation | Segments of DNA on two different chromosomes are exchanged. This can lead to altered gene regulation or the production of novel fusion genes, which can have phenotypic effects. | | Insertion | A segment of DNA is inserted into a different location in the genome. This can lead to alterations in gene expression or the creation of new genes, which can have phenotypic effects. | | Inversion | A segment of DNA is flipped, reversing the order of genes. This can lead to altered gene regulation or the production of novel fusion genes, which can have phenotypic effects. | ## Sources of CNV 1. Non-allelic Homologous Recombination NAHR (Non-allelic Homologous Recombination) is a process that can lead to deletions or duplications in the genome during meiosis, or production of germ cells. * From NAHR, resulting germ cells with deletion (more severe, clinical symptoms) 12 * or duplication NAHR theory supported by presence of segmental duplications ## Deletion and Duplication * **De Novo Deletion:** A deletion that occurs spontaneously and is not inherited from a parent. * **Inherited Duplication:** A duplication inherited from a parent. ## CNV types | Type | Description | | --------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Duplication | A segment of DNA is duplicated, resulting in an extra copy of the genes within that segment. This can lead to an increase in gene expression and potentially to phenotypic changes. | | Deletion | A segment of DNA is deleted, resulting in a loss of genes within that segment. This can lead to decreased gene expression and potentially to phenotypic changes. | | Translocation | Segments of DNA on two different chromosomes are exchanged. This can lead to altered gene regulation or the production of novel fusion genes, which can have phenotypic effects. | | Insertion | A segment of DNA is inserted into a different location in the genome. This can lead to alterations in gene expression or the creation of new genes, which can have phenotypic effects. | | Inversion | A segment of DNA is flipped, reversing the order of genes. This can lead to altered gene regulation or the production of novel fusion genes, which can have phenotypic effects. | ## Clinical Impact * Gene dosage: dosage sensitive gene * Genomic imbalances: congenital anomalies ## What types of genes are found to be copy number variable? * Brain development and activity * Immune system These two functions that have evolved rapidly in humans tend to be enriched in CNVs and tend to be spared ## What types of genes are found to be copy number variable? * Early development and some genes involved in cell division These tend to be spared ## Summary of key differences: CNVs vs NON-CNVs | Feature | CNVs | Non-CNVs (Inversions & Balanced Translocations) | | --------------- | ------------------------------------------- | -------------------------------------------------- | | Dosage Effect | Yes (gain or loss of genetic material) | No (structural change without dosage effect) | | Types | Deletions, duplications, insertions | Inversions, balanced translocations | | Mechanism | Unequal crossing over, replication slippage | Chromosomal breaks and rejoining, recombination | | Impact | Can lead to disease via dosage sensitivity or genomic imbalance | Can affect gene function or regulation, may cause problems in offspring during reproduction | | Clinical Examples | Cri-du-chat syndrome, Prader-Willi syndrome, Charcot-Marie-Tooth disease | Hemophilia A, balanced translocations linked to Down syndrome or Klinefelter syndrome | ## CNVs that cause disease * Fragile X Syndrome: * **Cause:** Trinucleotide CAG repeat in the FMR-1 gene on the X chromosome. * **Copy number of this sequence increases.** * **Appearance:** Portion of chromosome X is dangling by a thread * **The encoded protein (FRP, Fragile X Protein) is decreased in neuronal expression, leading to DISEASE** ## GENETICAL STUDIES ### Causes of Autism * Single gene, Mendelian * Cytogenetic * "Common autism" (multiple genes, environment) * Linkage, association and GWAS studies have only recognized a small number of consensus regions. * Multiple Genes acting either independently or perhaps synergistically. * Genome-wide Arrays ~8% diagnostic yield in ASD at EGL. * Rare and private variations may represent a considerable portion of the genetic components involved in ASDs. ## Copy Number Variants in Extended Autism Spectrum Disorder Families Reveal Candidates Potentially Involved in Autism Risk * **THE TESTED HYPOTHESIS IS by identifying CNVs that segregate in distantly affected relatives they would unearth novel ASD susceptibility genes with a moderate to strong effect** ## Importance of CNV * Genetic mechanism leading to phenotypic heterogeneity * Opportunity to expand GWAS (gene dosage, functional implications of SNP variation) * Association to numerous human disorders ## Mapping and identification of CNV * Hunting for genes underlying common diseases * Study familial genetic conditions * Contribute to a more accurate and complete human genome reference sequence used by all biomedical scientists. * Exclude variation found in unaffected individuals, helping researchers to target the region that might contain chromosomal rearrangements causing developmental defects ## Technologies: * aCGH, NGS, q-PCR, FISH ## CNV and SNP | Category | CNV (Database of Genomic Variants, http://projects.tcag:.ca/variation/) | SNP (dbSNP, http://www.ncbi.nlm.nih.gov/SNP/) | | ------------------------- | ------------------------------------------------------------------------- | ------------------------------------------------------- | | Total number | 38,406 (Mar 11, 2009) | 14,708,752 (Build 129) | | Size | 100 bp to 3 Mb | Mostly 1 bp | | Type | Deletion, duplication, complex | Transition, transversion, short deletion, short insertion | | Effects on genes | Gene dosage, interruption, etc. | Missense, nonsense, frameshift, splice site | | Percentage of the reference | 29.74% | <1% | | genome covered | | | ## Distributions of SNPs ### What can SNPs tell you? * Linkage Disequilibrium * Recombination * Association Studies * LD Mapping of complex traits * Fine Mapping * Demographic events * Identifying candidate genes * Study Selection