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Post by djoser-xyyman on Nov 26, 2018 15:28:36 GMT -5
Assembly of a pan-genome from deep sequencing of 910 humans of African descent--Rachel M. Sherman 2018
We used a deeply sequenced dataset of 910 individuals, all of African descent, to construct a set of DNA sequences that is
present in these individuals but missing from the reference human genome. We aligned 1.19 trillion reads from the 910
individuals to the reference genome (GRCh38), collected all reads that failed to align, and assembled these reads into contiguous
sequences (contigs). We then compared all contigs to one another to identify a set of unique sequences representing
regions of the African pan-genome missing from the reference genome. Our analysis revealed 296,485,284 bp in
125,715 distinct contigs present in the populations of African descent, demonstrating that the African pan-genome contains
~10% more DNA than the current human reference genome. Although the functional significance of nearly all of
this sequence is unknown, 387 of the novel contigs fall within 315 distinct protein-coding genes, and the rest appear to
be intergenic.
Since its initial publication1,2 , the human genome sequence has undergone continual improvements aimed at filling gaps and correcting
errors. The latest release, GRCh38, spans 3.1 gigabases (Gb), with just 875 remaining gaps3
. The ongoing effort to improve the human reference genome, led by the Genome Reference
Consortium, has in recent years added alternate loci for genomic regions where variation cannot be captured by SNPs or small insertions
and deletions (indels). These alternate loci, which comprise 261 scaffolds in GRCh38, capture a small amount of population
variation and improve read mapping for some data sets. Despite these efforts, the current human reference genome
derives primarily from a single individual4 , thus**** limiting its usefulness for genetic studies****, especially among admixed populations,
such as those representing the African diaspora. In recent years, a growing number of researchers have emphasized the importance
of capturing and representing sequencing data from diverse populations and incorporating these data into the reference genome
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Dating admixture events is unsolved problem in multi-way admixed populations --Emile R Chimusa Joel Defo Prisca K Thami
Abstract
Advances in human sequencing technologies, coupled with statistical and computational tools, have fostered the development of methods for dating admixture events. These methods have merits and drawbacks in estimating admixture events in multi-way admixed populations. Here, we first provide a comprehensive review and comparison of current methods pertinent to dating admixture events. Second, we assess various admixture dating tools. We do so by performing various simulations. Third, we apply the top two assessed methods to real data of a uniquely admixed population from South Africa. Results reveal that current dating admixture models are not sufficiently equipped to estimate ancient admixtures events and to identify multi-faceted admixture events in complex multi-way admixed populations. We conclude with a discussion of research areas where further work on dating admixture-based methods is needed.
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Post by djoser-xyyman on Nov 26, 2018 15:32:48 GMT -5
Super-man!? There is a reason why Africans are genetically advanced. As I said many time. 150,000years head start. Nature got it right
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Although the functional significance of nearly all of this sequence is unknown, 387 of the novel contigs fall within 315 distinct protein-coding genes, and the rest appear to
be intergenic.
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Post by djoser-xyyman on Nov 26, 2018 17:08:42 GMT -5
This is the first time I have seen this....East Asian genomes has so much similarity to African .....
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Quote:
"Our findings here demonstrate that the standard human reference genome lacks a substantial amount of DNA sequence compared with other human populations. The APG sequences contain 296.5 Mb, equal to 10% of the genome, regions that will necessarily be missed by any efforts relying only on GRCh38 to study human variation, as nearly all studies do at present. Of these 296.5 Mb, 120.7 Mb were shared by the Korean or Chinese populations, suggesting those regions ***may have been lost*** more recently or may be rare in the specific populations represented in GRCh38. Overall these results suggest that a single reference genome is not adequate for population-based studies of human genetics. Instead, a better approach may be to create reference genomes for all distinct human populations, which over time will eventually yield a comprehensive pan-genome capturing all of the DNA present in humans.
"
xyyman comment: No! They weren't "lost"!!!? They were removed for deception or to provide a Eurocentric spin
"The African pan-genome (APG) contigs have been deposited at NCBI under accession PDBU01000000 to provide a better foundation for future analyses of individuals of African ancestry." oHH!!! not found!
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Post by kel on Nov 28, 2018 0:30:11 GMT -5
'Super-man!? There is a reason why Africans are genetically advanced. As I said many time. 150,000years head start. Nature got it right'
Exactly right. Literally....more evolved...higher mutational load.
Superman ??
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Post by anansi on Nov 28, 2018 5:08:19 GMT -5
But wouldn't geographically closer West Asians proved to be more similar or am I missing something.
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Post by zarahan on Nov 28, 2018 21:01:55 GMT -5
I hope any so called "reference genome" is an honest sampling of African diversity,
north, south, east and west, as African, rather that yet another "true negro" or stereotyped
"sub-saharan" construct, even as they are careful to define a "Eurasian" "reference databank"
very broadly. We know the game: narrow- stereotyped "Africans" and broad-based "EUrasians."
Where have we seen this manipulative dodge befo?
Nevertheless the study above does say:
"Overall these results suggest that a single reference genome is not adequate for population-based studies of human genetics. Instead, a better approach may be to create reference genomes for all distinct human populations, which over time will eventually yield a comprehensive pan-genome capturing all of the DNA present in humans."
^^True if one is conceived as the be all and end all, but is the proposed "multiple genomes"
for "distinct human populations" simply blather to obscure the same old stereotyping?
Yeah, we don't have "just ONE" but "multiple."Break out the champagne! Uh huh. And then they
run the the same "multiple" as a repackaging of old, stereotyped concepts.
They say:
"Our findings here demonstrate that the standard human reference genome lacks a substantial
amount of DNA sequence compared with other human populations.
^^Sure, which opens up the alternative that the "one" can be built up over time with many more
samples to capture more of that diversity. THis does not necessarily call IN other words broaden
and deepen the One. This does not necessarily call for multiple databases.
A one genome concept is not necessarily a bad thing. One, STILL could have several variations,
so it is conceivable that multiple strands of diversity can be identified and seen
WITHIN the "one." Given past history, manipulation and obfuscation may still be at
work despite talk of multiple genomes. I am skeptical, based on past experience with
these people, and their manipulation.
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Post by zarahan on Nov 28, 2018 21:11:15 GMT -5
" Despite these efforts, the current human reference genome derives primarily from a single individual.."
What single individual they talking bout?
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Post by djoser-xyyman on Nov 28, 2018 21:55:27 GMT -5
a European ...who else. Same as the rCRS. Based upon a European female line although they realize their mistake and an new mtDNA refrence...based upon Africans ...as it should be. " Despite these efforts, the current human reference genome derives primarily from a single individual.."What single individual they talking bout? |
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Post by djoser-xyyman on Nov 28, 2018 22:00:02 GMT -5
"West Asian" is ambiguous. This is seen in many databases. eg in Henn's work "on backmigration to North Africa" paper. She and many researchers prefer to use Bedouins and not Khazars in the Levant because many people in the Levant are not indigenous. But wouldn't geographically closer West Asians proved to be more similar or am I missing something. |
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Post by djoser-xyyman on Nov 28, 2018 22:01:11 GMT -5
Super=genetically advanced 'Super-man!? There is a reason why Africans are genetically advanced. As I said many time. 150,000years head start. Nature got it right' Exactly right. Literally....more evolved...higher mutational load. Superman ?? |
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Post by kel on Nov 29, 2018 14:12:38 GMT -5
Super=genetically advanced  |
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Post by africurious on Nov 29, 2018 22:15:49 GMT -5
" Despite these efforts, the current human reference genome derives primarily from a single individual.."What single individual they talking bout? The ref genome is the genome of a random guy who gave a blood sample in response to an ad. It was his dna scientists sequenced when it was said that the “human genome” was sequenced. His dna is now the standard aka reference genome for humans. I read somewhere that he may’ve been a black American too. |
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