Jordans Notes 14 Flashcards
what is the biggest consequence of allelic drop out
and null alleles?
calling an individual as homozygous but it is actually heterozygous but one allele wasn’t amplified
false parentage determination etc.
What is homoplasy in microsatellites?
where two different individuals have what appears to be the same allele but it may have mutated to be the same length separately
doesn’t necessarily indicate relatedness
What is different between sequence level analysis
of genotyping vs sequencing?
sequencing looks at the entire sequence produced
genotyping only looks at single nucleotide substitutions (variants)
what is association mapping?
determining whether a genetic variant is associated with a certain trait or disease
What 3 types of studies can SNP genotyping be
used for
- Association mapping (traits)
- population genetics (including parentage)
- Evolution/adaptation
What does GBS stand for?
Genotyping by sequencing
What does RADseq stand for?
Restriction-site-Associated DNA sequencing
What does ddRAD stand for?
double digest Restriction-site-Associated DNA sequencing
what does using a restriction enzyme digest
achieve?
reduces the genome of all individuals to the same subset
What are the 5 steps of GBS?
- Restriction enzyme digest (reduce genome complexity)
- Adapters ligate to “sticky ends”
- PCR amplifies restricted fragments
- Fragments sequenced by Illumina HiSeq
- SNPs discovery
What do the sticky ends created during restriction
enzyme digest allow?
The ligation of adapters
What are the two types of adapters for SNP
genotyping?
barcode adapter and common adapters
What are the barcoding adapters for in SNP
genotyping?
sample identification (allows multiplexing)
What are the 4 steps of SNP discovery?
- raw sequences read to select highest quality reads
- Demultiplexing using barcode adapters
- high quality reads aligned
- alignments scanned to find SNPs
What are the 8 steps of RADseq?
- digest
- ligate first adapters
- pool DNA and shear randomly
- ligate second adapters
- Size select 300bp
- PCR fragments
- Sequence with MiSeq
- SNP discovery
What is demultiplexing?
separating different samples from a pooled product using barcode adapters
What are three pros of reduced representation
sequencing?
- greater depth of coverage at restricted loci
- greater number of samples for the same budget
- doesn’t require a reference genome
4 cons of reduced representation sequencing?
- large genome=low depth of coverage
- creating DNA library is expensive
- association mapping require annotated reference genome
- needs very high quality DNA
Why are SNPs more useful than microsatellites?
more loci examined increases accuracy despite lower variation between alleles
SNPs are usually in coding regions so can determine genomic regions of natural
selection
What is used to determine the contribution of a
SNP to a continuous trait?
Quantitative Trait Loci Mapping
