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Flashcards in Y chromosome Deck (27)
1

How many base pairs does the haploid autosomal nuclear DNA have?

3,2 billion bp (giga bp)

2

How many bases does the mtDNA have?

16 569 base pairs

3

What determines sex?

  • 7-8 weeks embryo - development of reproductive duct system
  • SRY gene (testis determination factor) - undifferentiated gonad --> testis
  • testis development - secretion of testosterone - external male genitalia
  • Müllerian inhibiting hormone (MIH) = a hormone produced by testis --> breakdown of Müllerian (female) ducts in embryo

4

why does the Y chromosome look the way it does?

It occured in four evolutionary steps, each involving a failure or recombination:

  1. from nascent to as in monotremes: recombination failure leading to deneration and shrinkage of the affected Y chromosome part; the affected area is no longer able to recombine with the X chromosome
  2. from as in monotremes to as in marsupials: recombination failure triggering more decay of Y chromosome
  3. from marsupials to as in monkeys: recombination failure, further shortening
  4. from as in monkeys to as in humans: further shrinkage
  5. SRY moved to short arm at unkown time point

5

Name some characteristics of the Y chromosome

  • haploid
  • is acrocentric (one short and one longer arm)
  • contains many repetitive DNA seqences
  • 60MB long
  • unique for men
  • paternally unchanged inherited
  • mutations may cause changes
  • 95% do not undergo recombination
  • pseudoautosomal PAR region
    • PAR1 and 2 undergo recombination during meiosis

6

How many genes does the Y chromosome contain?

78 genes, whereof:

  • SRY gene
  • 8 other genes specific for Y chromosome
  • 27 Y-specific protein coding genes
  • 16 housekeeping genes
  • MSY - male specific regions on the Y chromosome

7

Why is there such a low number of genes on the Y chromosome?

Because there is no recombination

8

Why can mutations easily be passed on to the next generation?

Because there is no correction of genes since there is no chromosome cross-linking

9

How does the Y chromosome get rid of mutations?

  • 8 genetic palindromes
  • forward or reversed order
  • 1/4 euchromatic DNA in the male genes
  • a sort of back up

10

Y STRs

  • most found on the q arm
  • approximately 300 Y-STRs
  • 200 billalic Y SNPs
  • 1 minisatellite MSY1

11

what is the Y chromosome used for?

  • tracing male migration patterns
  • evolutionary studies
  • population structure
  • human identification
  • forensic applications

12

How many markers should be used according to SWGDAM?

11

(9 minimal plus two more)

13

Name some Y-STRs

  • DYS19
  • DYS389I
  • DYS389II
  • DYS390
  • DYS391
  • DYS392
  • DYS393
  • DYS438
  • DYS439
  • DYS385a/b

14

What are the advantages of using a multiplex of several markers?

  • several markers are amplified simutaneously --> one standard
  • cross border comarison possible
  • smaller amounts of DNA are used --> saving of sample material

15

Name two commercial kits

PowerPlex Y and AmpflSTR Yfiler

16

How is the Y chromosome used in forensic analysis?

  • male DNA can be detected in samples containing both male and female DNA
  • DNA from several men
  • Sex determination (amelogenin)

17

How is the Y chromosome used in paternal kinship?

  • paternity testing
  • kinship testing
  • missing person cases

18

Which male:female DNA ratio can still be handled by kits in terms of efficiency and sensitivity?

1:1000

19

What is the average mutation rate for Y-STRs?

1 in 10^3

20

What is the mutation rate of Y-SNPs?

1 in 10^9

21

Why are Y-SNPs suitable for haplogroup classification?

Because the very seldom mutate at the same position

Because they have a slower mutation rate

 

22

How are Y haplogroups determined?

  1. Y-SNPs - are more accurate than STRs
  2. Y-STRs - a statistical estimation is done

23

What is a haplotype?

A haplotype is a set of genetic markers, inherited simultaneously

24

What are haplogroups?

Haplogroups are groups of haplotypes with certain specific common mutations

25

The amelogenin gene

  • deletion of six base pairs in X chromosome
  • different number of base pairs
  • reveals the sex of the specimen

26

Why do we use the Y chromosome in forensic genetics?

  • most violent crimes are commited by males
  • mixtures of male DNA with high levels of female DNA - differential extraction not necessary
  • lower discrimination capacity. Diversity only derived from mutations due to lack of recombination
  • paternal lineages

27

How can you distinguish between male relatives?

There are rapid mutating Y-STRs (RM Y-STRs) that increase the power of discrimination to 60%