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2nd year sem 1: Forensic Genetics > Lecture 7: Y chromosome > Flashcards

Lecture 7: Y chromosome Flashcards

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1
Q

Lineage markers are ___ as discriminative as autosomal markers

A

not

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2
Q

Are lineage markers useful as forensic markers?

A

possess some features which make them useful

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3
Q

whats the difference between autosomal DNA markers and Lineage markers?

A

Autosomal DNA markers are shuffled with each
generation
Lineage markers passed down generations

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4
Q

when do lineage markers change?

A

if theres a mutational event

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5
Q

whats the lineage marker for the Y chromosome called?

A

patrilineage

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6
Q

lineage markers are passed down from?

A

generation to generation

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7
Q

can you use the product rule when calculating random match probability ?

A

no

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8
Q

when do mutations arise?

A

during the DNA copying process

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9
Q

are mutations random?

A

yes

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10
Q

mutation rates for a Y-STR are between ?

A

10^-3 and 10^-4 per locus per generation.

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11
Q

How many Y chromosomes do males have?

A

1

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12
Q

How much of the human genome is contained in the Y chromosome ?

A

2%

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13
Q

how long is the Y chromosome?

A

50-60 Mb

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14
Q

what male specific functions odes the Y chromosome code for?

A

sex determination and spermatogenesis

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15
Q

what are the 2 main regions for the Y chromosome ?

A
  1. pseudo- autosomal regions (PAR 1 and PAR 2)

2. Male specific Y region (NRY)

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16
Q

whats the euchromatic region?

A

chromatin that exists in an extended state containing genes that may or may not be expressed

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17
Q

what’s more constant in size the euchromatic region or heterochromatic region?

A

euchromatic regin - 23 Mb

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18
Q

in meiosis when does the genetic crossing over occur and what doe sit lead too?

A

prophase 1, leads to new gene combinations.

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19
Q

The Y chromosome does not have _____ chromosome.

A

homologous

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20
Q

Does a large region of the Y chromosome recombine with the X chromosome ?

A

only a very small region

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21
Q

what’s located on the tip of the short arm?

A

pseudo-autosomal region one (PAR 1)

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22
Q

where is PAR 2 located?

A

distal end of the long arm.

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23
Q

whats avoided when looking for suitable forensic markers, for Y chromosome ?

A

regions of the Y-chromosome that share homology with the X chromosome

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24
Q

on the Y chromosome what is diversity due to?

A

due to mutation alone due to the lack of recombination

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25
Q

diversity on the Y chrosome terms?

A

haplotype (STRs) or haplogroups (SNP or Alu element insertion)

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26
Q

whats a haplotype/group?

A

collection of alleles that are linked (inherited together)

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27
Q

Name 3 Y polymorphisms?

A

β€’ Y-VNTRs β€’ Y-STRs β€’ Y-SNPs

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28
Q

what do VNTRs consist of?

A

MSY1 consists of a repeat unit of 25 bp. Polymorphism of 48-118 repeats.

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29
Q

Autosomal VNTRs contain a lot of what?

A

GC

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30
Q

MSY1 is __ AT

A

75%

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31
Q

The first reported Y-STR was in ?

A

1992

32
Q

what was the first reported Y-STR?

A

DYS19

33
Q

can the product rule for statistical calculation cannot be used on Y-VNTRs and STRs?

A

no , loci linked, discrimination power low.

34
Q

Y chromosome can be described as what?

A

hemizygous in nature

35
Q

whats hemizygous?

A

single-copy locus there is only one allele present

36
Q

Y-chromosome loci are multi-copy producing?

A

2 alleles

37
Q

Using STR loci with a higher mutation rate could do what?

A

distinguish close male relatives

38
Q

what are Bi-allelic markers?

A

Alu element insertion (YAP) and Single nucleotide polymorphisms (SNPs).

39
Q

what the the smallest and most abundant type of human polymorphism.?

A

SNPs

40
Q

slowly mutating SNPs involve into what ?

A

specific haplogroups, sometimes known as (UEPs)

41
Q

Y-SNPs play an important role in what studies?

A

migration studies.

42
Q

Y-SNP haplogroup tree is _______ changing.

A

continually

43
Q

haplogroups may be useful in predicting what?

A

predicting population of origin or even surnames!

44
Q

what was the first Y-STR Multiplexe?

A

First kit was Y-PLEX in 2001

45
Q

quantification kits are available to determine the following.

A

– Total human DNA
– Total male DNA
– Assessment of DNA degradation
– Identify PCR inhibition.

46
Q

How can you calculate the frequency of a halpotype?

A

using haplotype databases.

47
Q

whats the equation for calculating the observed haplotype?

A

𝑝 = X/N

48
Q

what can you do when a haplotype has not been observed in the database before?

A

estimate of the frequency can be done with an upper bound 95% confidence interval 3/N

49
Q

confidence interval can be applied to the calculated haplotype frequency using what equation?

A

𝑝 + (1.96 SR (p) (1βˆ’π‘) / N)

50
Q

How else can a confident internal be applied?

A

Clopper-Pearson method which is employed on the haplotype

databases.

51
Q

For sexual assault cases whats swabbed and why?

A

female genital tract in order to obtain an autosomal profile of the offender.

52
Q

what are two methods that can be sued to separate male and female DNA?

A
  • cytological detection in combination with laser microdissection
    of sperm cells
    -differential lysis in combination with sperm elution
53
Q

To obtain a meaningful profile or positive result what needs to be in the sample?

A

sufficient number of spermatozoa

54
Q

what happens when autosomal typing is non-successful ?

A

Y-STR may be used to give extra information about the male component of the mixture.

55
Q

when is ti important to use Y-STR to give extra info?

A

with azoospermic males or in samples where semen is not the biological fluid present.

56
Q

The detection of male epithelial cells may be important in cases where what?

A

where semen and spermatozoa are absent

57
Q

when may semen and spermatozoa be absent?

A

οƒ˜ cases of digital penetration
οƒ˜ no ejaculation
οƒ˜ azoospermic donors (vasectomised or infertile
individuals)

58
Q

what does Y-STR profiling do?

A

target the male contributor in mixed samples and can yield a male profile, even in 1000-fold excess of female DNA.

59
Q

whats an advantage of using YSTR profiling over autosomal STR kits?

A

Y-STR = identification of multiple male donors in a sample.

60
Q

when is RM Y-STR useful?

A

if paternal relatives need to be identified.

61
Q

whats the most common gender typing loci?

A

amelogenin locus

62
Q

what does amelogenin locus encode for?

A

proteins involved in tooth enamel formation

63
Q

how many homologous genes does amelogenin locus have? where and what are they?

A

2, one on each of the sex chromosomes which differ in size and sequence depending on if it is on the X (AMELX) or Y-chromosome (AMELY).

64
Q

In order to use the amelogenin locus to gender type what needs to be detected?

A

6 bp deletion on the AMELX locus

65
Q

How do we interpret the results of gender typing?

A

presence of just one fragment = X chromosomes alone, whereas two fragments indicate a male gender with a X and Y-chromosome.

66
Q

Some males have been found to have _____ of the AMELY locus

A

deficiency .

Y-STR typing useful to identify gender

67
Q

what are the preferred type of STRs and why?

A

Autosomal STRs will always be preferred over Y-STRs due to the discrimination power.

68
Q

How can a paternity test be done if the suspected father can not provide a sample?

A

Other relatives of the putative son can be tested, e.g. paternal uncles.

69
Q

what’s the first thing that gets collected for Mass-disaster Identification and Missing persons cases?

A

Direct references can be collected such as personal effects (tooth brushes and razors), and biological specimens (bloodstain cards).

70
Q

what happens if during Mass-disaster Identification and Missing persons cases theres no biological samples?

A

parentage testing can be performed using reference blood samples collected from parents and relatives.

71
Q

what does the Y chromosome also give information on?

A

bio- geographical ancestry

72
Q

what chromosome do paternal relatives share?

A

Y

73
Q

when is familial searches used?

A

used for the most serious offenses and DVI.

74
Q

when was familial searches developed?

A

developed by FSS (2002)

75
Q

why do familial search results undergo genetic testing?

A

they undergo Y-STR profiling, to eliminate false inclusions and re2duce intrusion and unnecessary direct contact with nominated, putative relatives.

76
Q

in what famous case was Y chrosome markers used to trace the paternal line?

A

Thomas Jefferson had a son with slave sally, in 1802. testing done in 1998 proved he was the father, by testing Y chrosome of 19 people.

77
Q

where can y

Y chrosome be applied?

A
  1. Forensic analysis of sexual assault cases with mixed male-female DNA profiles.
  2. Gender Identification of Amelogenin Y (AMEL Y) deficient males.
  3. Paternity deficiency cases.
  4. Missing persons investigations.
  5. Human migration and evolutionary studies.
  6. Historical and genealogical research.
  7. Used as an additional genetic test for familial search candidate lists.

2nd year sem 1: Forensic Genetics (8 decks)

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