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I'm a PhD student in bioinformatics working on genomic data, and I was wondering:

If I have access to a person's chromosomes, is there an assay that can determine that two chromosomes come from the same parent, or do I need to sequence their DNA, refer to statistical genomics and infer the ethnic group of each chromosome?

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  • $\begingroup$ ‘Have access to their chromosomes’ - what does this mean? What kind of data do you have? $\endgroup$
    – user438383
    Jun 14, 2021 at 13:15
  • $\begingroup$ @user438383 I meant more theoretically - if I had access to samples of a person's DNA. My current dataset it mutations under the form of a vcf file. $\endgroup$
    – Whitehot
    Jun 14, 2021 at 15:03
  • $\begingroup$ Does this answer your question? What can you learn about someone's mother and father by examining their DNA? $\endgroup$ Jun 16, 2021 at 3:47
  • $\begingroup$ @MaximilianPress although your answer to that question does provide some information towards answering mine, I don't think they are duplicates as such. For starters I am looking for quite technical answers, preferrably based on current literature, whereas OP in the linked question was looking for much broader information. $\endgroup$
    – Whitehot
    Jun 16, 2021 at 9:16
  • $\begingroup$ If that is your goal, I would suggest posting instead on bioinformatics.stackexchange.com. Biology SE is more likely to address your question at a higher level with a range of methodologies, such as the linked answer. $\endgroup$ Jun 16, 2021 at 16:50

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There is an implicit assumption in the question that current technology can obtain the correct sequences for each of the two homologous chromosomes (for all chromosome pairs) of a diploid individual. That is beyond the state of the art today.

In a few special circumstances, the latest methods can begin to approach that goal. For instance, where the parents of the individual are from highly distinct populations such as subspecies, and the populations have good sequence characterizations, then some have come close to resolving the separate sequences of homologous chromosomes. See, for example, "Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle" and "Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (Felis catus) and Asian Leopard Cat (Prionailurus bengalensis)".

Even when the genomes of the individual's two parents are also available (a set called a "trio"), correctly resolving the complete sequences of the individual's homologous chromosomes is difficult. See for instance, "Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios".

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  • $\begingroup$ Interesting, I knew that it was a complex task but not that it was that challenging! I am using 1000 Genomes project data, and in this paper wellcomeopenresearch.org/articles/4-50 they describe how they created SNP data for both chromosomes in each pair, in the "Phasing and imputation" section. Do you think that this data is unreliable? $\endgroup$
    – Whitehot
    Jun 16, 2021 at 9:24
  • $\begingroup$ I would quibble with this answer: obtaining phased diploid assemblies is an active research area and has been more or less achieved at quite good accuracy, e.g. nature.com/articles/s41587-020-0711-0. See also nature.com/articles/s41467-020-20536-y $\endgroup$ Jun 16, 2021 at 16:44
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    $\begingroup$ @Whitehot the phasing/imputation approaches that you mention are reliant on the linkage of alleles in the population- they are likely to be more or less accurate at the level of the population, but not terribly accurate at the level of the individual. Full, reasonably accurate individual-level haplotypes require long reads or in vivo linkage data (e.g. Hi-C), or ideally both. See refs in my other comment. $\endgroup$ Jun 16, 2021 at 16:47

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