Two unusual samples in 1000 genomes

Question

[linnaean]

Has anyone detected anything unusual about samples NA20289 or HG02789 in the 1000 genomes dataset?

There seems to possibly be phasing error in NA20289 (and perhaps HG02789 as well). Is there a way to detect phasing errors after the fact?

Additionally, NA20289's sister, NA20341 is listed as a mother and NA20342 as a father, but they do not have a child. Why would this be entered into the pedigree information if there is no genetic relationship between NA20341 and NA20342?

Thanks!

Answer 1

[Kevin Blighe]

I do not see anything unusual in the pedigree information that I have got:

FID   IID      PID  MID     Gender  Phenotype   Population  Relationship    Siblings    SecondOrder
2471  NA20289  0    0       2       0           ASW         mother          NA20341     0
2471  NA20290  0    NA20289 2       0           ASW         child           0           NA20341
2487  NA20341  0    0       2       0           ASW         mother          NA20289     NA20290

That says to me that:

1. NA20289 and NA20341 are sisters (and both mothers).
2. NA20289 is the mother of NA20290
3. NA20341 is the aunt Mary of NA20290

I do not see any connection to NA20342:

FID   IID      PID     MID Gender Phenotype Population  Relationship    Siblings    SecondOrder
2488  NA20342  0       0   1      0         ASW         father          0           0
2488  NA20343  NA20342 0   1      0         ASW         child           0           NA20332

NA20342 is the father of NA20343, but they have a different FID than the other samples, and no IDs overlap.

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That said, some of the African super group samples (of which the ASW sub-group is part) behaved unusually when I looked at PCA bi-plots of the entire cohort:

[from: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2 ]

However, it is understandable that there would be much genetic overlap between certain groups.

Kevin

[linnaean]

This is great, thanks!

Sorry, meant to say NA20340 is in the 2487 family with NA20341 where they are listed as father and mother but there are no children (hence they're not part of a duo or trio). Do you know why that would be recorded?

[Kevin Blighe]

Hey, yes, I have this for NA20340:

FID   IID     PID     MID  Gender Phenotype Population Relationship Siblings    SecondOrder
2487  NA20340 0       0    1      0         ASW        father       0           0

So, this guy is a non-blood Uncle Joe of NA20290, and [I assume], partner of NA20341.

I'm not sure why they are listed as father and mother, but maybe they have another child unlisted in the study.