{"id":3339,"date":"2017-05-13T12:21:43","date_gmt":"2017-05-13T12:21:43","guid":{"rendered":"http:\/\/www.jmhartley.com\/HBlog\/?p=3339"},"modified":"2017-05-15T11:08:23","modified_gmt":"2017-05-15T11:08:23","slug":"part-5-raw-dna-from-5-siblings-and-a-mother-a-new-and-improved-method","status":"publish","type":"post","link":"http:\/\/www.jmhartley.com\/HBlog\/2017\/05\/13\/part-5-raw-dna-from-5-siblings-and-a-mother-a-new-and-improved-method\/","title":{"rendered":"Part 5 \u2013 Raw DNA From 5 Siblings and a Mother – A New and Improved Method"},"content":{"rendered":"

In my last Blog, Part 4<\/a>, I found that I needed to go back to improve a method from an earlier step to make a later step work much easier. This did two things:<\/p>\n

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  1. Gave me a cleaner database<\/li>\n
  2. Set me back a ways<\/li>\n<\/ol>\n

    Re-do Principle 1: Homozygous Siblings<\/h4>\n

    I need now to create a new table. This will have the allele from Mom and Dad for each sibling. I copied my previous table to a new one called tblV1andV2HomozygousSibs. I opened my new table in design view and added the 10 new fields that I needed:<\/p>\n

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    The first five of the new fields will be have the Mom Patterns and the last five will have the Dad Patterns. Right now they are just blank. I’ll use an update query to add in homozygous alleles:<\/p>\n

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    This query says when my allele 1 is the same as allele 2 (homozygous), put allele 1 into the slot from my Mom and my Dad. The Dad slot goes off the page, but is there. When I run the update, it fills in over 485,000 lines. To do this by hand would have taken a while. This is the first step to filling in the Mom and Dad Patterns:<\/p>\n

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    I do the same query for each of my four other siblings. Care needs to\u00a0 be made the the right alleles are going in the right place. For example I wouldn’t want to put a Lori allele into a JonfromDad column. Then I check to see if the columns are filling in:<\/p>\n

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    If I recall right, this step fills in (or phases) about 8 million alleles. We don’t see any patterns yet other than AAAAA, but patterns are emerging in other parts of the table.<\/p>\n

    Step 2 – Homozygous Mom<\/h4>\n

    Here when mom has a GG for example, she would have to give a G to each child at that position, as that is all she has. I’ll use the Update Query again for this. Here is the Criteria:<\/p>\n

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    Here is the Update part:<\/p>\n

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    Step 3 – Heterozygous Siblings<\/h4>\n

    Here is an example:<\/p>\n

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    I have TC in my two alleles at this position as do my siblings. My mom must have had CC as she gave a C to each of her siblings. That leaves a T that we must have gotten from our dad. It looks like I may need 10 Update Queries for this one. Here is the criteria:<\/p>\n

    \"\"<\/a><\/p>\n

    The query says that Joelallele1 is not the same as Joelallele2 (Heterozygous Sibling) and I received my allele1 from mom.<\/p>\n

    \"\"<\/a><\/p>\n

    I update the table to say I got my other allele from my Dad. This is a little more complicated Update Query. I then reverse the Joelallele 1 and 2. When I get allele2 from mom, I get allele1 from Dad. Before I run the Update Query, I view it each time to see if there is a reasonable number of rows being updated. If no rows are updated, there is probably an error in my query. This update is in the 40-50,000 row range. Also, if I get values in the view panes, it often means I have put the results in the wrong field. Usually many empty rows in the view output is a good thing.<\/p>\n

    I forgot to copy and rename my Homozygous Sibs Table, so I just renamed it to tblV1andV2w3Principles.<\/p>\n

    Finding Patterns<\/h4>\n

    This time, I want to add ID’s to my patterns, so I’ll add two columns to my old Pattern Spreadsheet in Excel:<\/p>\n

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    Rather than do formulae for each pattern again, I’ll just scroll through my table to see if I can finesse the Pattern boundaries and add Position IDs.<\/p>\n

    Finessing Pattern Boundaries<\/h4>\n

    Here is an example at Chromosome 1 in the 77M range. There I had a change from ABBBB to ABABB. In my previous query, I only looked at Dad patterns where all the alleles were filled in. However, in the original pattern, we can infer the pattern even when alleles are missing.<\/p>\n

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    Previously, I had the change at the top row where there is a full pattern. However, in going from ABBBB to ABABB, we only need the first three positions to identify the pattern. And actually, we only need position 2 and 3 to identify ABABB. At ID 25839, there is an AGG??? Pattern. This has to be in the form of ABB<\/strong>BB. Then 4 lines later, is ?AG??. This has to be an ABA<\/strong>BB Pattern. Here is how I noted the change in the 77M range on my Excel Dad Pattern Spreadsheet:<\/p>\n

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    The DadStart and DadEnd columns have the refined Position numbers.<\/p>\n

    Refined Chromosome 1<\/h5>\n

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