Week 3.2: The Human Genome

Question 1

Human Genome

features (6)

Answer 1

• 3.05 billion bases
• linear nuclear genome
• circular mitochondrial genome (16.5 kb)
• average gene size = 27,000 bp
• 19,969 protein coding genesv (<2% of genome)
• 43,525 non coding genes (inconclusive)

Question 2

Telomere to Telomere Consortium

Answer 2

• reported complete sequence of female genome in 2022
• published human Y chromosome from HG 002 genome that corrects multiple errors in HG 38 Y chromosome and added over 30 million bp of sequence to reference
• potentially 0.3% errors

Question 3

Telomere to Telomere Consortium

CHM 13

Answer 3

special cell line almost completely homozygous for all chromosomes

Question 4

Human genome

Difficult sequencing areas

Answer 4

• centromeres and telomeres (heterochromatin)
• AT/GC rich regions
• palindromic sequences
• hairpin structures

Question 5

diploid

Answer 5

• An organism with 2 copies of each chromosome
• Human genome: 3.2 billion bases in each cell (haploid), 6.4 billion (diploid)

Question 6

Repeat sequences

sources

Answer 6

1. retroviruses
2. transposable elements (eg. Alu = 11% of genome)
3. simple repeat sequences

Question 7

transposable elements

Answer 7

• pieces of DNA that make self copies and insert elsewhere in genome
• can sometimes cause disease
• many have been present in genome for millions of years
• originally considered junk DNA, now a regulatory element

Question 8

genomic variant types

3

Answer 8

1. single nucleotide variant (SNV)
2. Insertions and deletions (indels)
3. structural variants (SV)

Question 9

single nucleotide variant
(SNV)

Answer 9

• smallest and most common genomic variant
• one nucleotide change at specific location in genome
• includes SNPs and rare single nucleotide differences
• may have SNP on one or both homologous chromosomes

Question 10

single nucleotide polymorphism
(SNP)

Answer 10

SNV that’s present in at least 1% of human population

Question 11

insertions and deletions
(indels)

Answer 11

• extra or missing DNA nucleotides in a genome
• typically < 50 nucleotides
• sometimes have larger impact on health and disease
• common type are tandem repeats

Question 12

indels

tandem repeats

Answer 12

• aka microsatellite
• short stretches of nucleotides repeated multiple times
• highly variable in size (2-3x to 100x)
• number of repeated units unique to each person and can be used for personal / relationship ID

Question 13

phased variants

Answer 13

Variants on same chromosome are linked together and inherited from one parent

Question 14

structural variants
(SV)

types (5)

Answer 14

1. large tandem repeats (repeated unit >15 bp)
2. copy number variants (CNV)
3. inversions
4. insertions
5. translocations

Question 15

structural variants

inversion

Answer 15

segment is inverted within chromosome

Question 16

structural variant

insertion

Answer 16

segment deleted from one chromosome and added to different chromosome

Question 17

translocation

Answer 17

segments that transfer (swap) between different chromosomes