Notes in LE012 DNA Diagnostics: Genomics

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Published	10/04/2024	If a somatic cell divides 5 times, you would expect roughly {{c1:: 5}} mutations
Published	10/04/2024	Sanger Sequencing {{c1:: Isolate a pure DNA fragment in a tube}}Anneal radioactive primers to single stranded DNAAdd polymerase + dNTPs + ddNTP termin…
Published	10/04/2024	Sanger Sequencing Isolate a pure DNA fragment in a tube{{c1:: Anneal radioactive primers to single stranded DNA }}Add polymerase + dNTPs + ddNTP termi…
Published	10/04/2024	Sanger Sequencing Isolate a pure DNA fragment in a tubeAnneal radioactive primers to single stranded DNA {{c1:: Add polymerase + dNTPs + ddNTP termina…
Published	10/04/2024	Sanger Sequencing Isolate a pure DNA fragment in a tubeAnneal radioactive primers to single stranded DNA Add polymerase + dNTPs + ddNTP terminators. D…
Published	10/04/2024	Automated Sanger Sequencing A {{c1:: read}} is the string of contiguous bases {{c2:: generated by one sequencing reaction}}
Published	10/04/2024	Automated Sanger Sequencing The {{c1:: read length}} is the {{c2:: number of contiguous bases generated by one reaction}}
Published	10/04/2024	Automated Sanger Sequencing The {{c1:: error rate}} is the fraction of bases that are {{c2:: read incorrectly by the sequencer}}
Published	10/04/2024	What was the main limitation to first generation sequencing methods?
Published	10/04/2024	Automated Sanger Sequencing The {{c1:: sequencing throughput}} is the number of bases that can be {{c2:: interrogated per unit time/labor}}
Published	10/04/2024	Why was DNA sequencing not a very useful tool for mapping human disease genes in the 20th century?
Published	10/04/2024	What was the downside to using targeted gene sequencing to map disease genes in the 20th century?
Published	10/04/2024	We refer to the genome sequence generated by the public project as the {{c1:: “reference genome”}}.
Published	10/04/2024	What was the first genome-wide technology to be developed?
Published	10/04/2024	DNA hybridization purpose
Published	10/04/2024	In DNA hybridization, {{c1:: probes}} are {{c2:: single-stranded DNA molecules}} called {{c3:: “spots” or “features”}}
Published	10/04/2024	Using DNA hybridization, how could we compare two samples to each other?
Published	10/04/2024	When designing an RNA expression array, the probes would be designed to target {{c1:: exons}}
Published	10/04/2024	When designing a genomic array to interrogate the whole genome, the probes would be {{c1:: evenly spaced everywhere}}
Published	10/04/2024	What method is the mainstay for cancer and clinical genomics?
Published	10/07/2024	Array comparative genomic hybridization (array-CGH){{c1:: Competitive DNA hybridization}} {{c1:: Scan: measure fluorescence}}{{c1:: Map copy number va…
Published	10/04/2024	What is the advantage to SNP genotyping with bead arrays instead of array-CGH?
Published	10/04/2024	Why haven’t polygenic risk scores been widely implemented in clinical practice?
Published	10/04/2024	DNA microarrays are {{c1::highly parallel}} meaning that {{c2::millions of loci can be interrogated simultaneously}}
Published	10/04/2024	DNA microarrays have limited {{c1:: resolution}} meaning that there is a {{c2:: limit to how many probes we can put on a microarray}}
Published	10/04/2024	Array design requires {{c1:: prior knowledge}} of genes/loci/SNPs
Published	10/04/2024	What genetic alterations cannot be detected with microarray?
Published	10/04/2024	How much does it cost to sequence a human genome in 2024?
Published	10/04/2024	How did second generation sequencing revolutionize the field?
Published	10/04/2024	What was the first revolution of Illumina sequencing?
Published	10/04/2024	What was the second revolution of Illumina sequencing?
Published	10/04/2024	What was the third revolution of Illumina sequencing?
Published	10/04/2024	DNA sequencingThe advantage to longer reads is that they are much more {{c1:: powerful}} than short reads
Published	10/04/2024	What is the main advantage to DNA sequencing over microarrays?
Published	10/04/2024	Challenges to Genome Assembly{{c1::Reads are short}}{{c2::The human genome is large, complex, and laden with repetitive elements}}{{c3::When repeat si…
Published	10/04/2024	Alignment of the {{c1:: “read pair”}} to the {{c2:: reference genome}} gives {{c3:: coordinates}} describing where in the human genome the read-pair c…
Published	10/04/2024	How do we distinguish genome variation from sequencing and alignment errors?
Published	10/04/2024	The number of times, on average, that teach base in the genome is sequenced is termed {{c1:: coverage}}
Published	10/04/2024	The industry standard for Illumina genome sequencing is {{c1:: 30X}} coverage relative to the haploid reference genome. Since our genomes are diploid,…
Published	10/04/2024	{{c1::Loss of heterozygosity}} can be observed at heterozygous germline SNVs.
Published	10/04/2024	{{c1:: Indels}} are a common source of {{c2:: loss of function mutations}}
Published	10/04/2024	Duplications and deletions (copy number variants, CNVs) can be identified as genomic regions with {{c1:: significantly altered read depth}}
Published	10/04/2024	{{c2::Structural variants}} can be identified based on the {{c1:: novel sequence junctions}} that define their “breakpoints”
Published	10/04/2024	Deletions, duplications, amplifications, inversions, insertions, translocations & complex rearrangements larger than 50bp in size are classified a…
Published	10/04/2024	What are the 2 main challenges that remain before whole genome sequencing becomes mainstream?
Published	10/04/2024	{{c1:: Clonal evolution}} generates {{c2:: intra-tumor heterogeneity}}
Published	10/04/2024	A tumor is not a single entity but a {{c1:: collection of related cell lineages}}
Published	10/04/2024	What is a main consequence of intra-tumor heterogeneity?
Published	10/04/2024	For complex and highly polygenic human traits, what does causal gene discovery require?
Published	10/04/2024	What is the “rule of thumb” to power genome-wide analysis?
Published	10/04/2024	Genome diversity is the {{c1::rule}} not the {{c1::exception}}
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