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EVE 131 Human Genetic Variation & Evolution > EVE 131 > Flashcards

EVE 131 Flashcards

1
Q

Who developed UNIX?

A

Ken Thompson, Dennis Ritchie, and some others developed UNIX in 1969 using a PDP-7 at Bell Labs (R&D company that developed computer operating systems)

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2
Q

Who is Richard Stallman and what is he known for?

A
  1. 1985 - Richard Stallman founded the FSF (Free Software Foundation/GNU (GNU’s Not Unix))
  2. 1988 - FSF creates GPL (General Public License)
    • GPL is important in that it allows users to freely runs tidy, share, and modify the software
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3
Q

When was the first Linux kernel completed?

A

In 1991 by Linus Torvalds

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4
Q

What is GUI?

A

GUI stands for Graphical User interface

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5
Q

Who developed and founded early human genetics?

A
  • Gregor Mendel came up with pedigrees that helped identify diseases under Mendelian Inheritance
  • In early human genetics, the primary focus was on diseases and transmission
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6
Q

Describe RFLP

A

RFLP stands for Restriction Fragment Length Polymorphism

  • RFLP is a technique that analyzes DNA to identify variations in DNA sequences between individuals
    • Extracted DNA from individuals are treated with a restriction enzymes
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7
Q

What are restriction enzymes?

A

Restriction enzyme (REs) are used to fragment DNA
- This can help in creating genetic markers to help location pieces of DNA that are adjacent to specific sequences of variants

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8
Q

What is the first gene for a disease sequenced?

A

1989: Cystic Fibrosis gene, AKA CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene was sequences via positional cloning:
- codes for a transmembrane protein
- Most commonly found in the European population
- An in-frame 3 base pair deletion causes the mutation that causes cystic fibrosis

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9
Q

What is positional cloning?

A

When pieces of DNA around the region of DNA you think a certain gene is at is cloned.

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10
Q

When was the Human Genome Project initiated?

A

1990

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11
Q

What was the first human chromosome sequenced?

A

Chr. 22
- Later found to be LARGER than chr. 21 but the order was left to how it was already set

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12
Q

When was Phase I of the HapMap project completed and what was the goal?

A

Completed in 2005, goal was to identify variable/polymorphic sites on the same chromosome amongst individuals from 11 different populations

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13
Q

Who was the first individual genomes sequenced?

A

Venter (and also Watson) in 2007-2008

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14
Q

When did 23and Me offer autosomal DNA genotype to consumers?

A

2007

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15
Q

What are homologs and why would they differ?

A
  • Homologs are copies of a PARTICULAR chromosome
  • They can differ due to:
    1. Mutations
    2. Recombinations
    3. Indels
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16
Q

Describe the size and major components of the human genome such as genes and pseudogenes

A

The human genome is ~3.1Gb
- It contains ~22,000 genes and 10,000 pseudogenes

17
Q

Which strand is the coding sequence on?

A

The coding sequence can be on EITHER strand: + or - strand

*Depending on if coding sequence is on the + or - strand, will also determine if it will be forward or reverse transcribed

18
Q

What is TP53?

A

TP53 is a tumor suppressor gene responsible for regulation the cell cycle
- This gene is involved in cancer

19
Q

Is the X or Y chromosome larger?

A

The X chr

20
Q

What are the uses and properties of pedigrees?

A
  • Used to represent relationships between individuals
    Properties:
    • Every child has 2 parents
    • “Founders” are the individuals with missing parents in the pedigree
    • Consanguinity (mating between close relatives) creates loops or 2 bars (in medical pedigrees)

*Pedigrees are loosely correlated with GENETIC sharing and more correlated with GENEALOGICAL sharing

21
Q

What is a matrix and why may it be useful?

A

A matrix is used to numerically represent a pedigree
- EACH individual has a unique index
- For founders, their parents = 0

  • A matrix is useful in calculating kinship coefficients
22
Q

Describe the Random Mating Model

A

Developed by Joe Chang, helps to show the number of shared ancestors in a pedigree:
- Each diamond is a monogamous couple
- Each member of the couple chooses parents at random from the previous generation
- If there is a SINGLE line stemming from a diamond (a couple) that means the parents are siblings

23
Q

How can you find the average number o generations until a common ancestral family exists in a population of size N?

A

log(base 2)N

Ex: In a population of 5.5 million, a family to every living individual in this population first existed: log(base 2)(5,500,000) == 22 generations ago (22 x 20.5 = ~450 years)

*Keep in mind this is assuming CONSTANT population size over the years which is probably unrealistic as population size has been increasing every since
- After ~5-6 generations, an individuals will still be genealogical ancestors but no longer genetic ancestors

24
Q

What is the general kinship formula with NO loops?

A

(1/2)^ (i + 1)

*i = # of matings separating relatives

  • This gives the probability of 2 RANDOMLY chosen genes being IBD
25
Q

Describe the inbreeding coefficient

A

The inbreeding coefficient is denoted by (f (subscript of individual))
- It is the probability that the two gene copies in an individual’s genome at a given locus are IBD
- f = kinship coefficient of the parents

*If parents are NOT related, the inbreeding coefficient = 0 = kinship coefficient

26
Q

Describe the relatedness coefficient

A

The relatedness coefficient is the average proportion of the genome shared IBD between relatives

*In order to calculate the relatedness coefficient, you must know BOTH individuals’ inbreeding coefficient (f) + kinship coefficient between both individuals

27
Q

What is a kinship coefficient?

A

Kinship coefficient is denoted by ϕ , and is the probability IBD of 2 randomly chosen alleles from each of 2 individuals

28
Q

What are the required molecules for Sanger sequencing reactions?

A
  1. ssDNA
  2. 4 dNTPs (All 4 in all 4 tubes)
  3. 4 ddNTPs (1 in each of the 4 tubes)
  4. DNA polymerase
29
Q

What does 1st generation sequencing include?

A

1970s had 2 approaches for first generation sequencing:

1.Sanger sequencing: sequence by synthesis using DNAP

2.Maxam-Gilbert: DNA degradation sequencing (cutting bases off to determine sequence)

30
Q

What is 2nd generation sequencing?

A

Illumina:
- No ddNTPs
- Includes DNA bridge amplification using a flow cell and cluster generation

31
Q

What is contained in SAM files?

A

SAM files:
- contains raw reads
- can get FAST Q file from this
- has info. about how the sequences are positioned in the genome

32
Q
A

EVE 131 Human Genetic Variation & Evolution (1 decks)

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