Final Exam - Things to Memorize

Question 1

YFS:
- common name
- genus
- species
- NCBI TaxonID
- number of haploid chromosomes
- haploid genome size

Answer 1

• common name: domestic dog
• genus: canis
• species: canis familiaris
• NCBI TaxonID: 9615
• number of haploid chromosomes: 39
• haploid genome size: 2.4 billion (Gb)

Question 2

name the 3 key advancements in single cell technology

Answer 2

• integrated fluid circuits
• nanodroplets
• barcoding

Question 3

draw the molecular techniques that allow us to achieve cell resolution

Answer 3

• cell barcode, UMI, sample index
• P5, 97

Question 4

what molecular techniques that allow us to achieve cell resolution, why?

Answer 4

• cell barcode, UMI, sample index
• they allow you to identify the individual cell and differentiate the cells

Question 5

what is the purpose of P5 and P7 adapters?

Answer 5

they are oligo binding sites for sequencing

Question 6

nuclei advantages in single cell

Answer 6

• sample processing logistics
• less stress and mitochondrial signal

Question 7

cell advantages in simple cell

Answer 7

• more complete transcriptions
• detection sensitivity
• better connection to translation

Question 8

what are the four major downstream analyses of single cell transcriptomic data?

Answer 8

• differential expression
• gene enrichment analysis
• cell-cell communication
• trajectory analysis

Question 9

mutations can be:

Answer 9

• harmful
• beneficial
• neutral

Question 10

define sensitivity

Answer 10

trying to discover all the real variants

Question 11

define specificity

Answer 11

limiting the false positives that creep in when filters get too lenient

Question 12

how many probes does infintum 1 have, how many does infinium 2 have?

Answer 12

• infintum 1 = 2
• infinium 2 = 1

Question 13

what are 2 metrics we use for looking for errors (QC) in SNPS?

Answer 13

• call rate per SNP (indicate genotype quality)
• call rate per individual (indicate DNA quality)

Question 14

power is influenced by: (4 things)

Answer 14

• sample size
• distribution of effect sizes
• frequency
• linkage disequilibrium

Question 15

telomere to telomere assembly recipe

Answer 15

1. error correction of accurate long reads
2. assembly graph construction
3. graph simplification with ultra long reads
4. phasing and scaffolding

Question 16

We define the pangenome of based on 3 “A” components, what are they?

Answer 16

• Assemblies
• Alignments
• Annotations

Question 17

pros and cons of low coverage WGS and high coverage exome

Answer 17

• WGS: pro=cost effective, con=less accurate variant calls
• exome: pro=more accurate variant calls, con=only sequencing 2% of the genome

Question 18

what is the equation to determine the frequency of a variant in a general population?

Answer 18

1/2N

Question 19

equation for false discovery rate

Answer 19

FDR= FP/FP+TP

Question 20

what is the biological reason that explains how each individual can carry so many bad variant (in one word)?

Answer 20

redundancy

Question 21

• what are the 4 things in gene regulation?
• what two are dictated by the cell?
• which two can be influenced by the researchers choices?

Answer 21

• what, when, where, and how much
• what and how much = cell
• when and where = researcher