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bm210 biochemistry > C3&4 human genome project > Flashcards

C3&4 human genome project Flashcards

1
Q

genome

A

complete set of chromosomes

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2
Q

what does every genetic and physical marker have

A

a specific locus in genome

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3
Q

what was the goal of the human genome project

A

-determine the seq of the 3 billion chemical base pairs in human DNA
-identify all genes in human DNA to their position on chromosomes
-attempt to predict the function of all genes
-utilise this info for understanding of disease, developing better medicine

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4
Q

name given to those who participated in mapping and sequencing process

A

formal international consortium

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5
Q

phase 1 of human genome project

A

produce high resolution chromosomal maps
-position genetic markers (and genes)
-create libraries of BAC clones for sequencing (physical map)

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6
Q

phase 2 of human genome project

A

sequence each BAC DNA

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7
Q

phase 3 of human genome project

A

assemble all sequences to produce final draft and annotate to identify genes

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8
Q

overview of human genome project (7 steps)

A
  1. genomic DNA (2 male, 2 female)
  2. BAC library (250,000bp)
  3. organised mapped large clone contigs
  4. BAC to be sequenced
  5. shotgun sequence
  6. assembly
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9
Q

what maps are combined to order all BACs

A

genetic and physical

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10
Q

what is old sanger sequencing

A

radiation
4 separate dideoxy reactions
one for each base, very slow, manual reading of results off x-ray fillm

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11
Q

new sanger sequencing

A

like PCR but with fluorescent terminators
-run products on gel
-separated by size
-laser scans bands (ACGT)

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12
Q

second phase genome project

A

-used these advances in sanger DNA sequencing technology and reduction in cost
-computational assembly of all sequences into ‘contig’

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13
Q

how to provide one-fold coverage

A

requires ~3 million separate sequencing reactions producing 1000 bases each

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14
Q

draft sequence coverage

A

4 fold

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15
Q

finished sequence coverage

A

9 fold

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16
Q

what is IHGSC

A

clone by clone approach

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17
Q

advantages and disadvantages of IHGSC

A

-very effective at getting over regions of highly repetitive DNA sequences
-able to retrieve clones later

-slow process
-expensive

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18
Q

what is celera

A

shotgun sequencing
blast genome into small fragments, sequence each one and then use the power of computers to reassemble sequence

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19
Q

what did celera have to rely on

A

public databases of sequence and mapping information in order to assemble the sequence that was generated by this method

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20
Q

completion of human genome

A

-june 2000 white house announced 80% sequenced
-working draft publication made available on web july 2000
-publication of 90%
-completion of 99.99% july 2003

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21
Q

how many genes (original 2001 answer)

A

20,000-25,000 genes
~1.5-5% of the genome

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22
Q

genetic variation between humans is visible at the genomic scale

A

population genetics

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23
Q

how many chromosomes were sequenced

A

10 (5 people)

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24
Q

what were the two major types of revelation

A

single nucleotide polymorphisms (SNPs)
copy number variants (CNVs)

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25
Q

what is the international hapmap project

A

finding the more common SNP varients in the worlds population

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26
Q

how many human SNPs in nature in 2005 were reported to HapMap

A

> 1 million

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27
Q

what 4 populations of people were studied in HapMap project

A

270 people
nigeria (african)
japan and china (asian)
utah (northern & western european ancestry)

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28
Q

how many gaps were in the original human genome project

A

8%

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29
Q

who published the final results of the HGP

A

telomere to telomere (T2T) consortium

30
Q

the draft ‘T2T-CHM13’ annotation totals

A

63494 genes
233,615 transcripts

31
Q

what increases in complexity as you climb the evolutionary tree

A

transcript/protein structure

32
Q

6 things learned in HGP

A

1.how do humans compare to other species
2. humans are evolving
3. fine structure of inheritance
4. human (pre)history
5. way in which our genes control our response to medication
6. disease genes

33
Q

what is comparative genomics and evolution

A

comparisons with other species is possible to determine evolutionary relatedness
and understanding of evolutionary changes in genes/proteins

34
Q

what methods are used to comparative genomics

A

-sequence alignments across species
-genome based phylogenies

35
Q

organism genome comparison (smallest to biggest genes)

A

E.coli- 4,200
S. cerevisiae (yeast)-6,000
C. elegans (nematode)- 14,000
D. melanogaster (fruit fly)- 14,000
A. thaliana (mustard plant)- 24,000
Mammalian- 20,000-25,000

36
Q

what allows novel genes/proteins during evolution

A

modular domains

37
Q

many pathways are highly what across species

A

conserved

38
Q

what is TBC1D3

A

only found in humans
regulates growth factors and role in RAS-mediated cancers

39
Q

examples of selective expansion in protein families and domains

A

-immune function
-intercellular signalling
-metabolic function
-olfaction
-haemostasis
-apoptosis
-neural function
-translation

40
Q

how many genes with human specific features vs how many entirely human specific genes

A

850
50+

41
Q

what kinds of genes show evidence for fast/recent evolution in humans

A

-pathogen response
-cell cycle/DNA metabolism
-protein metabolism
-reproduction
-neuronal activity
-skin pigmentation

42
Q

2 gene selections showing evidence for fast/recent human evolution

A

HBB gene selection
haemoglobin B (anaemias)

LCT gene selection
lactase gene variants selected for in early human groups which used milk in diet

43
Q

how do most HIV strains enter cells

A

using CCR5 as main co-receptors (with CD4)

44
Q

how do some people have natural resistance to HIV infection

A

homozygous for ∆ 32 mutation on CCR5 gene

45
Q

what is the paradox of CCR5 ∆32 variant prevalence

A

distribution requires millennia but HIV only around since 1970/80s

46
Q

possible explanation for paradox of CCR5 ∆32 variant prevalence

A

∆ 32 may have been protected (been selected for in) ancestral populations against earlier HIV like epidemics or even small pox
NOT bubonic plague/yersinia pestis ass was once thought

47
Q

what is FOXP2

A

gene involved in human speech and language disorders
potentially critically involved in human specifiic development of language
2 aa changes between chimps and humans/neanderthals/denisovans

48
Q

example of human specific loss of sequences

A

olfactory genes

49
Q

how were LD blocks discovered

A

through the study of common variants

50
Q

term given to haploid genotype

A

haplotype

51
Q

how are haplotypes formed

A

formed by a collection of linked marker alleles on one chr that are inherited together

52
Q

over short distances how do haplotypes remain intact

A

not disrupted by meiotic reccombination

53
Q

what are the very short distances of haplotypes that remain intact called

A

linkage disequilibrium blocks
[LD blocks]
unit of inheritance

54
Q

where does chiasma formation in meiosis happen

A

hotspots
an LD block is the same in between

55
Q

what populations show highest levels of genetic polymorphisms

A

african

56
Q

every other continent has less genetic variation than africa but some from what

A

archaic humans

57
Q

what is mediated by genetic differences in terms of drug treatment

A

individual variation

58
Q

what factors are under genetic control in pharmacogenetics

A

-inactivation/activation by oxidative pathways (cytochrome P450s)
-conjugation for excretion through the kidney (GST)
-target sensitivity
-toxicity=side effects
-disease mutation type

59
Q

what is an advent of personalised/stratified medicine

A

identifying patients who will respond well to drug treatment

60
Q

pharmacogenomics knowledge applied with example

A

screening patients for CYP2C9 and VKORC1 gene varients identifies those who should start on a low dose of warfarin to avoid risk of internal bleeding

61
Q

what variants affect antidepressant escitalopram serum conc and treatment success

A

CYP2C19

62
Q

PegIFN-a-2b or PegIFN-a-2a combined with RBV for what treatment

A

hep c

63
Q

in terms of CF what is the most common mutation in european pops and what is the result

A

DF508
no protein produced

64
Q

in terms of CF what percentage of mutations just damage the function of the protein

A

5%

65
Q

in terms of CF what drug is used to restore function

A

ivacaftor

66
Q

8.5 in 100,000 users of flucloxacillin have what reaction

A

serious liver reaction called drug induced liver injury (DILI)

67
Q

what has been associated with DILI risk from flucolaxacillin

A

an SNP marker
rs2395029[G]

68
Q

what can be said about the SNP marker associated with flucolaxacillin (linkage)

A

marker in complete linkage disequilibrium [LD] HLA*7501 immune cell surface protein

69
Q

basic research practical uses of human genome project

A

all genes known forever
vast and integrated info set based on genome publicly available

70
Q

medical advances since human genome project

A

-pharmacogenomics; right drug for right people
-genome wide genetic studies offer best hope of cracking complex genetic disorders
-diagnostic tests

bm210 biochemistry (19 decks)

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