Is Reich Lab coming clean? - Extensive DNA database- WOWWW!

[djoser-xyyman]

Downloadable genotypes of present-day and ancient DNA data (compiled from published papers)


reich.hms.harvard.edu/downloadable-genotypes-worlds-published-ancient-dna-data


genome (in hg19 coordinates).

All data released here:
(a) have already been published (some by our group and some by other groups - see full list of references below),
(b) have permissions appropriate for fully public data release,
(c) are typed at a set of 1,233,013 sites in the genome (or 597,573 sites for present-day individuals genotyped on the Affymetrix Human Origins array). Typing is typically pseudo-haploid for ancient samples, when coverage is too low for full genotyping.

There are two datasets:
"1240K" : Ancient and present-day individuals (from either shotgun sequencing data or in-solution target capture, with a range of coverages) at 1,233,013 sites,
"1240K+HO": Data from the above set merged with present-day individuals typed on the Human Origins array with 597,573 sites.

Each dataset consists of four files, in eigenstrat format. For details, please see: eigensoft:
.anno: Rich meta-information for each individual.
.ind : Three columns: Individual ID, sex determination, and group label.
.snp : Information on each analyzed SNP position (SNP id, physical/genetic location and reference/variant alleles, where the reference allele matches hg19).
.geno: Genotypes.

This is a data release as of Fri Feb 22 12:25:37 EST 2019. We aim to continue to update this dataset over time.

Version 37.2
Description .anno .ind .snp .geno Tarball all files Notes
1240K link
(1.1Mb) link
(189Kb) link
(75Mb) link
(1.5Gb) link
(1.6Gb) 5081 individuals
(2107 ancient, 2974 present-day)1
1240K+HO link
(987Kb) link
(281Kb) link
(36Mb) link
(1.1Gb) link
(1.2Gb) 7744 individuals
(2107 ancient, 5637 present-day)1
1: includes one ancestral reference, and three present-day references: human, chimp, gorilla.



We would be grateful if users of this dataset could alert us to any errors they detect and help us to fill in missing data. This could include: (1) errors or missing information for location, latitude, longitude, archaeological context, date, and group label, (2) concerns about Y chromosome or mitochondrial DNA haplogroup determinations, and (3) evidence for other problems in the data or annotations for individuals. Please write to Swapan 'Shop' Mallick and David Reich with any suggestions. We would also be grateful if members of the community could suggest additional content that would be helpful to add to this page to make it maximally useful. Finally, please let us know if there is any ancient DNA data we should be including that we have missed.

[djoser-xyyman]

Is the criticism of Reich Lab making them open access to their database? It is amazing that most leading scientist that publish in major magazines have passed through the Reich Labs. They definitely have a monopoly of datasets.

Is Nicky P parting ways with David Reich? Is their a falling out. It did not get pass me that Nicky P had not part in that recent controversy. While Reich was plying hard ball Nicky P stayed clear of that kerfuffle. Is he now with the Broad Institute?

[djoser-xyyman]

www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=8;t=010113

Steppe Study

Here are reviewers telling researchers (in a paper that both Kraus and Reich seemed to have particpated in) that their theories don't match up with their own genomic data:

quote:
This hypothesis about the Caucasus source of Proto-Indo-European has been advanced also for slightly other reasons by David Reich and Kristian Kristiansen , so I think it should be elaborated here by the authors and they should marshall their new results to add whatever support they can.

However, this hypothesis should rest on showing a sustained admixture between Maikop and
Yamnaya to serve as a bridge to Yamnaya from the Caucasus (because the authors accept Yamnaya as connected to later PIE.) It is difficult to see in the results presented here a sustained gene flow from Maikop into Yamnaya, that would sustain this hypothesis . On lines 410 and 432 the authors preferred to see the Anatolian Farmer genes that appeared in Yamnaya as flowing from southeastern Europe, with a 20% WHG component, not from Maikop, without the WHG component. If most of the c.15% Anatolian Farmer found in Yamnaya came from the west, it leaves very little room for gene flow into Yamnaya from Maikop. If the 3% WHG that makes the difference between a western and Caucasian source of Anatolian Farmer is strongly supported by their data, that makes a Caucasian origin of PIE less likely because it reduces gene flow from Maikop into the steppes . In fact it suggests that very little south-to-north gene flow occurred during the Maikop period (except into 2 individuals from a distinct, small, local genetic group different from Maikop and Yamnaya). This is puzzling and unexpected, but also it fails to support the bridge that seems to be needed.


criticism?
static-content.springer.com/esm/art%3A10.1038%2Fs41467-018-08220-8/MediaObjects/41467_2018_8220_MOESM2_ESM.pdf

[djoser-xyyman]

Did Reich get the Noble prize? I don't think so. Remember my post on him wanting to receive the Noble prize was removed by Admin on ES just before before I was banned there.

[djoser-xyyman]

Reich Lab Mocked in the New York Times by Mansamusa

www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=8;t=010104


More seriously, he accusses Reich of being a part of an archaeogenteic oligopoly where they monopolize aDNA samples and bully smaller operations into handing over their samples or ceding control over to him of their research. The oligopoly is made of three labs: Reich's, Krause's and Paabo's. Their attitude towards collecting aDNA samples was likened to imperialists:

“Certain geneticists see the rest of world as the 19th-century colonialists saw Africa — as raw-material opportunities and nothing else."

Finally, the media is falling out of love with this man. It took long enough. One guy at Anthrogenica translated criticism of him in Portuguese and got banned if I remember correctly.

Reich Profiled in NYT
More on the alledged bullying of Reich's lab:

The landscape is dominated by four well-funded, well-connected labs, three of which — Paabo’s in Leipzig, along with those of two of his protégés, Reich at Harvard and Johannes Krause, who runs a newer outfit in the small German city Jena — collaborate closely with one another, to the point that some critics accuse them of collusion. The power of these top labs extends to samples, data and even technology: Proprietary chemical reagents let them isolate and enrich ancient samples much more accurately and cost-effectively than other labs can. One geneticist compared competing with the big labs to battling an entire navy “with a little dinghy, armed with a small knife.” Another told me: “A small lab focusing on a particular site would not be able to place their work in the context of the bigger picture. The only way I can get access to that data is if I give my bone to David or Johannes and wait until they process it — and bury me in the list of contributors to their paper.”

The selective pressure to collaborate with this state-of-the-art oligopoly is extremely strong, not only because of their advantages in funding, speed and operational scale but also because of the relationships they enjoy with the top-tier journals. Publication in a title like Nature or Science can utterly transform a young scholar’s career, enhancing both the prospect of tenure and the ability to secure grant funding. The rush to corner the market on old bones in some “understudied” place or time period has placed a high premium on virtually all samples, creating perverse incentives for researchers to procure these scarce, nonrenewable resources. The only entry fee for a 27th or 53rd author slot in this “free-for-all bonanza of Nature papers” (as one geneticist described it to me) is the cost of a bone shipment and a minimal account of its basic archaeological provenance. Multiple researchers told me that it wasn’t unusual for junior authors to be given just days to review a finished manuscript, with little input into its broader framing. (Reich, Krause and Paabo all dispute this, saying they couldn’t think of any examples in which co-authors were given such a short time to review a manuscript.)

[djoser-xyyman]

quote by xyyman on ES

"These guys have made and making so much money and the power involved. They are not changing their minds. Greed it at stake. Disgrace is the only option. Like what his "wife" did to that guy."

[asante]

Interesting to note that members are being banned from various sites for mere criticisms of those researchers. That is interesting, considering just how much of their research is parroted around on those forums as the gospel. It's almost as though their is a conspiracy to create some of those sites in order to steer the narrative in favor of those guys.

[djoser-xyyman]

steps

1. download files and unzip.

2. Create your parfile(txt)

reich2019.txt
------------
genotypename: v37.2.1240K.geno
snpname: v37.2.1240K.snp
indivname: v37.2.1240K.ind
outputformat: PACKEDPED
genooutfilename: reich2019.bed
snpoutfilename: reich2019.bim
indoutfilename: reich2019.fam

3. use convertf to create you PLINK bed, bim and fam files

command
$ convertf -p reich2019.txt

all files must be in the same directory



use convertf to create you PLINK bed, bim and fam files

reich2019.txt
------------
genotypename: v37.2.1240K.geno
snpname: v37.2.1240K.snp
indivname: v37.2.1240K.ind
outputformat: PACKEDPED
genooutfilename: reich2019.bed
snpoutfilename: reich2019.bim
indoutfilename: reich2019.fam


command
$ convertf -p reich2019.txt

[djoser-xyyman]

You now have PLINK fileset with 5081 individuals of which 50% are ancient humans including ancient Skoglund Africans. You now play with this genome set like using ADMIXTURE and looking at phenotypes

[djoser-xyyman]

Helena Malmstrom

www.ebi.ac.uk/ena/data/view/PRJEB9783