Part 7 – Raw DNA From 5 Siblings and a Mother – DNA From Mom

I’ve spent my last 6 Blogs on this topic finding out which alleles came from my dad. In this Blog, I would like to work on finding my siblings’ and my alleles that come from mom.

The Ironic Step of Phasing – Mom Alleles from Dad Alleles

I call this ironic step in that it was my mom that was tested for DNA. Based on her results we found out a lot of the alleles that her children got from our dad who passed away quite a while ago. Now, we use those alleles we got from dad to figure out which alleles we got from mom. From the Whit Athey Paper referenced at the ISOGG Web Page on Phasing:

If a child is heterozygous at a particular SNP, and if it is possible to determine which parent contributed one of the bases, then the other parent necessarily contributed the other (or alternate) base.

 

First I copy my FillinOne Table to a MomfromDadOne Table. Then I’ll do a query on that.

This says where I am heterozygous, and I have an allele from dad, I want to see where I’m missing one from mom.

I have over 50,000 of these which will be easy to update. I will want to put Joelallele2 in the blank where JoelfromDad = Joelallele1. Then I will want Joelallele1 in the JoelfromMom space when my allele from Dad is Joelallele2.

I ran this query twice for each sibling, so 10 times. This updated 50-60,000 alleles per sibling, so about a quarter of a million alleles altogether.

Finding Mom Patterns

Now that I have filled in more alleles from Mom, it should be easier to find Mom Patterns. Here is a Query to find Min and Max for the AAAAB Pattern:

Results in:

This saves a lot of time and gives me the start and stop positions of all the AAAAB Mom Patterns. In my previous look which I now see as premature, I only found 2 AAAAB Patterns. Now thanks to my MomfromDad update above, I have at least 17 AAAAB Patterns. The only drawback is that if there is more than one AAAAB Pattern within a Chromosome, it will not show that. However, if I run all the Mom Patterns, and find overlapping Patterns, that can be reconciled later. In fact, I see an overlap already:

The first AAAAB Pattern I found was 162-233M which I did see as large. I already had found an AAABA Pattern from 192-249M. This could mean that AAAAB goes from 162-192 and that the 233M AAAAB pattern was just an outlying singleton.

I also recall that I want ID’s, so I’ll add that to my query:

Because I have so much new information, I’ll put this into a new spreadsheet:

AAABA Mom Pattern

I just have to change the Query slightly to get the AAABA Mom Pattern:

The results of this Query go into the new spreadsheet. This spreadsheet will be sorted by Chromosome later.

I added a column for IDEnd minus IDStart:

Where this is zero, it would indicate a single Pattern.

I went through all the Mom Patterns and got a spreadsheet of 194 rows that need to be reconciled. Here are Chromosomes 1 and 2 sorted:

Reconciling Chromosome 1

I have added in a column for possible assignment of a crossover to a sibling. Note that up to about 20M everything looks OK. There are discrete Patterns. ABBBA to AABBA is a change in the second position which belongs to Sharon. The change from AABBA to AABBB goes to Lori. Then the AABBB is the same as BBAAA which goes to ABAAA. That would be my crossover [Joel].

I did a Query showing where all the alleles were filled in for the Mom Patterns:

This shows where my Crossover is at ID # 8984. I have added a few more columns to my Mom Pattern Spreadsheet to add the more refined cut points:

Next I’ll look at 77M.

As best I can tell, there are two single AABAB’s in the middle of an AABBB Pattern. Next I will want to find the start of that AABBB Pattern. To find that I do a query to look for the AABBB Pattern in Chromosome 1. That Query results in more AABBB Patterns.

A Problem

I have a problem in that it appears that the Mom Patterns of AABBB and AABAB appear to overlap each other on Chromosome 1. I assume that means that I did something wrong.

refilling the dad patterns

That means that I should go back and fill the Dad Pattern back in:

First I recreate a Fill-in Table using the old Three Principles Table. Then I do update queries on that. Hopefully these numbers will work:

Back to Mom Patterns From Dad Patterns

Just so I’m not going backwards, I’ll redo this step. I copied my revised fill-in Table to a revised Mom from Dad Table. This time I’ll keep track of the alleles for fun:

So in retrospect, I don’t know if I made a mistake with the Dad fill-in’s or in the Mom fill-in from the Dad Pattern. Hopefully, there were no mistakes this time.

 

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