This
is a continuation from my part 1 post at http://notjusttheparrys.blogspot.co.uk/2016/12/analysing-my-dna-crossovers-part-1.html.
My initial intention for this post was simply to look at the shared matches between
the siblings, to see how those results correlate with the phasing of chromosome
21 represented in part 1. That sounds
easy enough but one
of the reasons it has taken me so long to post, is that things very rapidly
become complicated!
So, in this post, I
will look at the shared matching between the siblings and their three closest
relatives - a niece, a first cousin and a third cousin once removed - and how
adding the additional relatives caused me to alter my interpretation of how the
niece matched.
This was my starting
point from part 1, the four siblings A, B, C, and D, with their chromosomes
represented by the four colours:
The parents'
chromosomes can then be represented as follows:
And which parts of
the parents' chromosomes each of the siblings received like this:
One of the closest
matches to the siblings is their niece, daughter of a deceased brother. Since the brother was never tested, I don't
know what crossover points he received from his parents. The niece will only
have one chromosome (of each chromosome pair) from her father - but the
differences in matching between the niece and the siblings could be as a result
of crossovers within each of her father's chromosomes, or between the father's
two chromosomes.
So these are the
comparisons between the niece and each of the siblings from Gedmatch, along
with a potential crossover point identified at 43:
So immediately there
is an issue - the niece matches sibling B up until 43, and, correctly, does not
match any of the other siblings until that point. However, beyond 43, the niece appears to
match none of the siblings (based on the grey "match" bar). But we know that, since sibling A and B do
not match each other at all on this chromosome, the two siblings A and B,
between them, cover all four of the siblings' parents' chromosome 21s. So, if the niece doesn't match sibling B,
then she has to match sibling A at least.
And, looking at the Gedmatch image, it seems quite clear that this is a
threshold issue - the niece does actually match the three siblings A, C and D
beyond 43. The match just isn't being
picked up as a match by Gedmatch at the default threshold. Reducing the threshold indicates the niece
matches all three siblings A, C and D by 6.9cM, containing between 1041 - 1045
SNPs.
The initial
interpretation of the DNA received by the niece therefore became:
Next, I looked at
how the siblings and the niece matched the siblings' paternal first
cousin. The Gedmatch image below was
produced using the default threshold,
but again, reducing the thresholds slightly indicated a potential matching
segment just below the 7cM threshold:
Chr Start
Location End
Location Centimorgans (cM)
21 14,677,076 22,936,413 18.2
21 22,950,552 33,423,011 15.7
21 34,132,054 37,056,381 6.7
The paternal first
cousin can only match the siblings through their father's chromosomes. But, as their father will not have received
exactly the same DNA as the first cousin's parent did, there will be some areas
where the first cousin does not match any of the siblings.
By comparison to the
phasing of the siblings and niece, the first cousin's matching segments were
therefore mapped as follows:
(this process also
indicated that the "Parent 2" phasing represents the siblings'
father's chromosomes.)
So far, so good.
When I downloaded
the matching segments for the siblings, in order to start investigating the
shared matches, I realised a known relative shared DNA with sibling B on
chromosome 21. The relative is a 3rd
cousin 1 removed (3c1r) and shares from about 17 to 28. The shared ancestry is on the siblings'
paternal side of the family, the same as the 1c is:
But now there's a
problem. This 3c1r does not match any of
the other siblings, or the niece, on chromosome 21. But, at the point where the 3c1r matches B, we have already
"used" both of the paternal chromosomes, one for the matching between
the first cousin and siblings ACD, the other for the matching between the niece
and sibling B. It's okay that the 1c
doesn't match the 3c1r - that actually indicates that the chromosome ACD share
with the 1c must be the one the siblings' father received from his mother, the
siblings' grandmother, as she is also a common ancestor with the 1c.
But, clearly the
chromosome the niece shares with sibling B cannot be the other paternal
chromosome. As far as I am aware,
there's no other shared ancestry with the 3c1r.
So, let's go back to the matching between the niece and the siblings -
where did I go wrong?
Siblings A, C, and D
all show a very small area of potentially matching SNPs between 24 and 26 - but
it is only 1.5 cM and 365 SNP. I don't
believe that has any significance, especially as there's no change in matching
with sibling B. (The niece only has one relevant chromosome in this comparison
- and the kit being used is a "paternal" one that's been phased using
her mother's data, so should be fairly accurate.)
So what about the
potentially matching segment with sibling C, between 37 - 39? This is a 4.2 cM segment, containing 743 SNPs
- so it is a small segment that, under normal circumstances, when matching to
unknown and more distant relatives, should be ignored.
From the sibling
phasing, B and C are matching from 37, after C had a crossover, and their
matching segment is a "Parent 1" segment. So, is it possible that the niece's matching
should actually be as follows:
The niece is
matching B on a Parent 1 chromosome (now known to be maternal). Sibling C then starts to match both B &
the niece at 37, but the niece stops matching C at 39, as the niece has a
crossover between the two chromosomes her father had. If she switches from her father's maternal
chromosome to his paternal chromosome, and those are also the two chromosomes
sibling B has, that would account for why the niece continues to match B until
43. At 43 there is then a crossover
between the two chromosomes of Parent 2 - which would indicate a crossover in
the niece's father, passed on to the niece within the segment from his paternal
chromosome. This interpretation would account for the niece's match to the 1c, between 40 - 43, and explain why she does not match the paternal 3c1r earlier on the chromosome, between 17 - 28.
If that is the
situation, then the diagram of the siblings' parents' chromosomes can now be
extended to also show the DNA received by their grandchild, the siblings'
niece, as well as the potential source for the paternal chromosomes:
Please
let me know if you can spot any mistakes in my reasoning.
