Quiz 2a-2023-BTGYkey.docx

1] ___ Genetic drift is strongest in: Large populations Small populations Stable populations Admixed populations None of the above 2] ___ In GWAS studies, the problem with using a standard P-value is that there would be many false positive results because of multiple testing. One approach to reduc...

1] ___ Genetic drift is strongest in: Large populations Small populations Stable populations Admixed populations None of the above 2] ___ In GWAS studies, the problem with using a standard P-value is that there would be many false positive results because of multiple testing. One approach to reduce this problem is: Bonferroni correction Jackknifing Bootstrapping Amplifying None of the above 3] ___In a GWAS result, when a TAG-SNP is significantly associated with the disease phenotype this indicates that: It causes the disease phenotype It is in linkage with the disease-causing allele It is polymorphic in controls It is fixed in the carriers none of the above 4] ___A ___________ block is a set of SNPs that are associated together. Sequence Domain Exon Gene Haplotype 5] ___Around 45% of the human genome is derived from repetitive elements. One of the most common types of these are ______________. Beta globins Ultra-conserved elements Hox genes L1 retrotransposons Promoters 6] ___The measure of effect size, or the strength of association P-value Fst Disparity Index Odds ratio Coefficient of linkage of disequilibrium 7] ___ The __________is the number of reads that map to a sequence at a specific position. Lambda Coverage Odds ratio N50 8] ___ One of the most effective in solution targeted enrichment strategies that enable construction of a DNA library with same specific regions of a whole genome from different samples uses ____________ to capture the desired sequences. Streptavidin and Biotin Flow cell Low-coverage sequencing Sbf and AbeKI Sanger sequencing 9] ___ The N50 is a metric used to provide information on the quality of an _________ . Alignment GWAS analysis Admixture Assembly 10] ___ Inbreeding reduces the frequency of: heterozygotes homozygotes the dominant allele the recessive allele the wildtype allele 11] ___ If there is strong population structure, then subpopulations will have very divergent allele frequencies and the ___will be high. Disparity Index (DI) Z-statistic (Z) Bootstrap Value (BS) Fixation Index (Fst) Gamma (G) 12] ___ Movement of individuals between populations followed by breeding is: inbreeding drift migration equilibrium transformation 13] ___ In a study of bobcats, there was evidence of adaption at GPR158 and TRPM3 based on Fst patterns consistent with ____________ the regions of chromosomes where these genes are found. Inbreeding in inheritance models of assortative mating low p-values from a GWAS in a selective sweep in 14] ___ In the ____________________ of inheritance, either one or two copies of allele A are required for a specific fold increase in disease risk. Common Dominant Model Recessive Model Additive Model Allele Model Genotype Model 15] ___ Which of these next generation sequencing platforms is the dominant system used today? Sanger Affymetrix 454 Illumina none of the above 16] ___The Illumina sequencing instruments work by: ligating adapters to DNA fragments that are then annealed to beads and undergo amplification in an emulsion before being distributed into honeycomb-like wells ligating adapters to DNA fragments that are bound to a dense lawn of oligonucleotides on a flow cell and undergo bridge amplification and then are sequenced in parallel passing a single DNA strand into a well that holds one polymerase molecule using the dideoxy method before passing product through capillary 17] ___ The quality of a nucleotide base call from an Illumina sequencer is provided in the fasaq file with its respective _________ coded using a single ASCII character: Phred score Base call Color score N50 score C value 18] ___ Advantages of GWAS studies to identify genes that affect phenotypes include: Can be applied to quantitative and complex traits Very dense SNP assays now available that covers nearly entire genomes Relatively inexpensive because the haplotype block structure of genomes mean you do not need to genotype all variants Do not need any prior information on pathways/genes that affect phenotype all of the above 19] ___ A _______________ trait is the result of cumulative action of many genes. Mendelian Environmental Quantitative Epigenetic none of the above 20] ___ Linkage disequilibrium is nonrandom association of: genes in a network invariant sites two or more alleles at one locus two or more alleles at two or more different loci none of the above