W10LECT - Introduction to genomics, Methods in genomics

Question 1

What are the features of genome?

Answer 1

• Genome is the entirety of an organism’s hereditary information.
• It is encoded either in DNA or, for many types of viruses, in RNA.
• The genome includes both the genes and the non-coding sequences of the DNA/RNA. In diploid cells, there are two genomes.

Question 2

What is Genomics?

Answer 2

Genomics is the study of the function, structure and interactions of the genome.
− Involves- methods, RNA, protein, bioinformatics.
− Can be- structural genomics, comparative genomics, plant genomics, human genomics,
pharmacogenomics or medical genomics.

Question 3

Data about the Human Genome
1. What is the percentage of protein coding and non-protein coding?

Answer 3

1.2% protein coding (the rest 98.8% is non-coding)

Question 4

Data about the Human Genome
2. Recombination is higher in male or female?

Answer 4

female

Question 5

Data about the Human Genome
3. Mutations are higher in male meiosis OR female meiosis?

Answer 5

Mutations are higher in male meiosis (the majority of mutations originates in males)

Question 6

Data about the Human Genome
3. Mutations are higher in male meiosis OR female meiosis?

Answer 6

Mutations are higher in male meiosis (the majority of mutations originates in males)

Question 7

Data about the Human Genome
4. How many new mutations in the offspring from the parents are there?

Answer 7

60

Question 8

Data about the Human Genome
5. how many loss-of-mutations in the annotated genes and genes involved in Mendelian diseases?

Answer 8

Every individual has 250-300 loss-of-function mutations in the annotated genes, among which 50-
100 genes are involved in Mendelian diseases.

Question 9

Data about the Human Genome
6. What is the percentage of repeats in human genome?

Answer 9

46% repeats, a lot of them are transponsons (i.e., jumping genes)

Question 10

Data about the Human Genome
7. What are the most frequent repeats?

Answer 10

Most frequent repeats are called Alu, which occupy 10.6%

Question 11

Data about the Human Genome
8. What is the largest gene? its role? Its size and location

Answer 11

• Largest gene: DMD, which codes for dystrophin
• size: 2,224,919 bases
• location: Xp21.2

Question 12

Data about the Human Genome
9. What is the longest coding sequence?

Answer 12

TTN, codes for titin; coding sequence: 104,076 bp; 34,692 amino acid

Question 13

Data about the Human Genome
10. What is the longest exon?

Answer 13

Longest exon: TTN: 17,106 bp

Question 14

Data about the Human Genome
11. What is the percentage of human genome is gene desert?

Answer 14

20% of the genome is gene desert (a region >500 kbp without a gene)

Question 15

Data about the Human Genome
12. What are the Gene rich chromosomes?

Answer 15

Gene rich chromosomes: 17, 19, 22 (richest is the 19, with 1,458 coding and 980 non-coding genes)

Question 16

Data about the Human Genome
12. What are the Gene poor chromosomes?

Answer 16

Gene-poor chromosomes: Y, 4, 13, 18, and X; (poorest is the Y with 72 coding and 137 non-coding
genes and < 1.0 gene/Mb)

Question 17

Data about the Human Genome
13. How many imprinted genes are known?

Answer 17

At present 156 imprinted genes are known

Question 18

Data about the Human Genome
14. The majority of SNPs found associated with ___

Answer 18

disease outside the coding region.

Question 19

Data about the Human Genome
15. Examples of diseases, where CNVs can play a role?

Answer 19

There are several diseases, where CNVs can play a role, like Crohn’s disease, Alzheimer disease,
autism, obesity, AIDS, etc.

Question 20

Data about the Human Genome
16. How can CNVs play a role in transplantation?

Answer 20

CNVs can play a role in transplantation.
=> If in the organ acceptor, owing to a CNV, a gene is missing, and the gene is present in the donor, a graft-versus-host disease can develop in spite of MHC identity, i.e. an immune response could develop against the gene product.

Question 21

Data about the Human Genome
17. In every cell type assessed, between 10 and 25% of human and mouse autosomal genes can be subject to ___

Answer 21

monoallelic expression (MAE).

Question 22

Data about the Human Genome
18. The majority of genes (75-90%) shows BAE, i.e. ___

Answer 22

both alleles are active in the cell, with the additional remark from above that at any point in time, a cell contains mostly transcripts from one allele.

Question 23

Data about the Human Genome
19. The majority of genes (75-90%) shows __, i.e. both alleles are active in the cell, with the additional remark from above that at any point in time, a cell contains mostly transcripts from one allele.

Answer 23

BAE

Question 24

Human Genome Project (HGP)
1. What are the features of Human Genome Project (HGP)?

Answer 24

• US government project coordinated by the department of energy and the national institutes of health (NIH)
• Formally began 1st October 1990
• Planned for 15 years
• Completed April 2003 (after 13 years)
• Paper published in 2006

Question 25

Human Genome Project (HGP)
2. What are the main roles of HGP?

Answer 25

Question 26

Human Genome Project (HGP)
3. How is HGP performed?

Answer 26

Question 27

Human Genome Project (HGP)
4. How do we perform sequencing?

Answer 27

• 1st generation (Sanger)
• 2nd generation (New generation, ie NGS = next generation sequencing or short-read sequencing, massively parallel sequencing)
• 3rd generation (Long-read sequencing)

Question 28

Encyclopedia of DNA elements (ENCODE)
1. What is Encyclopedia of DNA elements (ENCODE)?

Answer 28

A public research project which aims to identify functional elements in the human genome.
- Aim: to determine which regions are transcribed into RNA, which regions are likely to control the genes that are used in a particular type of cell, and which regions are associated with a wide variety of proteins.

Question 29

Encyclopedia of DNA elements (ENCODE)
2. What are the main Results of Encyclopedia of DNA elements (ENCODE)?

Answer 29

• 80% of the genome have biochemical functions, in particular outside of the well-studied protein coding regions.
• They first introduce NGS (Next Generation Sequencing).
• Disease-linked regions include enhancers or other functional sequences. And cell type is important.
• About 75% of the genome is transcribed at some point in some cells, and that genes are highly
  interlaced with overlapping transcripts that are synthesized from both DNA strand.
• 96% of CpGs exhibited differential methylation in at least one cell type or tissue assayed, and levels of
  DNA methylation correlated with chromatin accessibility.

Question 30

ENCODE: Searching for functional sites in the genome
3. How do we perform ENCODE: Searching for functional sites in the genome?

Answer 30

• Genome digestion with DNAse. If the enzyme accesses and digests, it is an open region, and other enzymes and molecules (e.g. transcription factors) also have access, i.e. a functional region.
• Next, sequencing around the cleavage site.

Question 31

Background Studying of Disease
1. What are the Two main types of Background Studying of Disease?

Answer 31

1. Hypothesis driven
2. Hypothesis-free

Question 32

Background Studying of Disease
2. What is Hypothesis driven?

Answer 32

Hypothesis driven- we know what gene we are looking for.
- There is preconception (i.e., idea).
- For example: candidate gene association studies.

Question 33

Background Studying of Disease
2. What is Hypothesis -free?

Answer 33

Hypothesis-free- screening of whole / some in population to look for a gene.
- No preconception.
- For example: genome wide association studies (GWAS), whole genome sequencing, microarray measurements for studying gene expression (genomic methods).

Question 34

Describe Gene deficiencies, KO people

Answer 34

• In mice 30% of gene deficiencies is in utero lethal
• Majority has phenotypic consequences
  – In average every individual lacks 20 genes (KO)
  – E.g. genes for smell, or redundant genes
  – Advantageous gene deficiencies:
  – LPA, FUT2, CCR5, PCSK9 KO
  – 43 genes whose inactivation is lethal to mice were found to be inactivated in humans who are alive and apparently well.

Question 35

What is the Most variable part of the genome?

Answer 35

• MHC: 4 million bp 6p21.3, >100 genes
• 10 times more variations than in other part of the genome. Evolutionary advantageous

Question 36

Explain „Single-cell transcriptomics”

Answer 36

• At any point in time, a cell contains mostly transcripts from one allele. It is independent of the parent of origin of the allele
• transcription in mammals is discontinuous and occurs in transcriptional bursts interspersed by refractory periods of gene inactivity.

Question 37

Explain „Single-cell transcriptomics”

Answer 37

• At any point in time, a cell contains mostly transcripts from one allele. It is independent of the parent of origin of the allele
• transcription in mammals is discontinuous and occurs in transcriptional bursts interspersed by refractory periods of gene inactivity.

Question 38

Explain Monoallelic expression (MAE)

Answer 38

• 10-25% of genes shows MAE (not imprinting)
• It is mitotically stable higher nucleotide diversity than genes with biallelic expression enriched for ones encoding proteins present on the cell surface and responsible for interactions between the cell and its environment
• Heterozygote advantage

Question 39

Describe Comparative genomics

Answer 39

• Comparing the genomes of contemporary species.
• Genes essential for life
• Gene essential for multicellular organisms.
• Genome regions conserved through the evolution.

Question 40

What are the features of Conserved regions?

Answer 40

1. Small differences between evolutionary distant species
2. Probably important functions
3. 99% of the protein coding genes in the mouse have human homologs. Difference ≈ 300 genes. At genomic level: 90%.
4. Chimpanzee: 96%, Y chromosomes are very

Question 41

What are the features of Genome of modern humans

Answer 41

1. The genome of homo sapiens mixed with other human species
2. Genomes of European and Asian people contain 1-4% Neanderthal genome
3. About 3–5% of the DNA of Melanesians and Aboriginal Australians and around 7%-8% in Papuans deriving from Denisovans.
4. Useful genes survived