Genome sequencing analysis

Question 1

Describe

The repeated sequences of the human genome

Answer 1

Almost 60% of the genome is repeated
* Transposons
* Repeat satellites that contract and expand
* Large segmental duplications

Question 2

Explain

Mapping vs alignment

Answer 2

Mapping quickly finds the best place(s) where a read can then be aligned optimally, at the base-level.

Question 3

What happens after the genome is indexed?

Answer 3

1. Exact matches are first found in the reference genome and used as seeds (regions where read is likely to align)
2. Co-linear (same order in both read and reference genome) and clustered seeds (for higher confidence) are kept and the alignment is extended.

Question 4

What are the different types of genomic variants?

Answer 4

• Single-nucleotide polymorphisms
• Insertion-deletion polymorphisms
• Structural variants

Question 5

What are the genomic variations in a typical human genome?

Answer 5

• 4.5M SNVs
• 650k indels
• 17k structural variants

Question 6

What is the point of studying genomic variants?

Answer 6

• Looking for pathogenic variants in undiagnosed rare disease patients
• Looking for common variants associated with a complex disease
• Understand human evolution and migration

Question 7

How are small variants identified?

Answer 7

Small variants are identified as recurrent differences between reads and the reference genome

Question 8

What technique is used to improve indel detection?

Answer 8

Read realignment: tools like ABRA2 can do that

Question 9

Explain

VCF format

Answer 9

Text-based format to record to position of variant, its alleles, confidence, misc information and genotype

Question 10

What are the advantages of using longer reads?

Answer 10

• Better structural variant detection
• Enable de novo gene assembly, to better identify complex variants

Question 11

Define

Pangenome

Answer 11

Collection of genomes and the genetic variants among them

Question 12

Define

vg

Answer 12

Variation Graph Toolkit
Open-source program for graph construction, read mapping and variant calling

Question 13

How do pangenome-based methods fare against traditional approaches?

Answer 13

Pangenome-based approaches are better, especially for insertions

Question 14

Give an example of a deletion

Answer 14

• The reads are correctly through the deletion on the pangenome
• Many reads are aligned to the linear reference with the end unaligned (soft-clipped)

Question 15

Describe

Building a human pangenome reference

Answer 15

• Use latest sequencing technologies for 350 diverse individuals
• Pangenome containing a comprehensive catalog of structural variants

Question 16

What are the six types of structural variants?

Answer 16

• Tandem duplications
• Insertions/deletions
• Short tandem repeat contraction/expansion
• Inversions
• Mobile element insertions
• Translocations