World Families Forums - Can someone define "phase" for us?

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geneticgenie
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« on: February 23, 2009, 02:01:10 AM »

Can someone explain haplotype phase, or phasing software? Or is phasing a slang term?

This is what Montgomery Slatkin says at
http://www.nature.com/nrg/journal/v9/n6/box/nrg2361_BX2.html

"The basic idea is that individuals that are homozygous at all loci or all but one locus provide some information about haplotype frequencies that can then be used to infer the haplotype phase of the other individuals."

This sounds like something we are already doing here albeit on a primitive level.

"There are several ways to determine haplotypes from genotypes; this is commonly referred to as resolving haplotype phase." He says that the program PHASE has performed the best in simulation studies.

When I look at my X results for the area including the centromere, I have many heterozygous readings, but if I pick the two most common haplotypes from all the male results, my parents fit very nicely just by guessing the most likely ones. Now would that also be called a way of resolving possible haplotype phase? 

Kathy J.
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Kathy J.
X Chromosomes: 75% English, 12.5% German, 6.25% Dutch, 3.125% Irish, 3.125% Scottish;
from Father's X: 43.75% English, 6.25% Dutch;
from Mother's X: 31.25% English, 12.5% German, 3.125% Irish, 3.125% Scottish
Seán MacGorman Powell
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« Reply #1 on: February 25, 2009, 08:54:23 PM »

Can someone explain haplotype phase, or phasing software? Or is phasing a slang term?

This is what Montgomery Slatkin says at
http://www.nature.com/nrg/journal/v9/n6/box/nrg2361_BX2.html

"The basic idea is that individuals that are homozygous at all loci or all but one locus provide some information about haplotype frequencies that can then be used to infer the haplotype phase of the other individuals."

This sounds like something we are already doing here albeit on a primitive level.

"There are several ways to determine haplotypes from genotypes; this is commonly referred to as resolving haplotype phase." He says that the program PHASE has performed the best in simulation studies.

When I look at my X results for the area including the centromere, I have many heterozygous readings, but if I pick the two most common haplotypes from all the male results, my parents fit very nicely just by guessing the most likely ones. Now would that also be called a way of resolving possible haplotype phase? 

Kathy J.


Sorry for the delayed response... I tried to answer this question a couple of days ago, but website glitches prevented me from being able to login...

Phasing isn't a slang term, it just means the process of trying to determine which DNA came from which chromosome of a homologous pair (i.e., determining which came from the mother, and which came from the father, as you've been doing).

Ann Turner has a good writeup of this concept here:

http://www.jogg.info/42/files/turner.pdf

Your guessing-based-on-common-results-from-males is one way of phasing, though I have no idea how the accuracy of that method compares with using programs like PHASE.

Sean
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Svaale
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« Reply #2 on: February 27, 2009, 05:36:49 PM »

I have only my own intuitive understanding of what phase means.

Usually when receiving data from population studies or your own data the data is not phased is not ordered maybe just sorted alphabetically and called genotypes. The process to seperate the genotype data into two haplotypes for later block comparisment each from your parent is called phasing.

There are two ways to find your haplotypes

1) Testing family members like parent-siblings pair by direct comparisment
2) Infering the haplotypes using unrelated invididuals from population databases

The first method is the most accurate as the comparisment is direct and not based on statistical methods. The second method have more uncertainty involved especially if your haplotypes are rare but in most cases works.

Please note that for method 2) there is still no way to tell which haplotype came from who of your parents unless they come from very distinct different genetic groups, and for method 1) there is no way telling from which of the grandparents the haplotype originate.
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