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Genetic Predisposition of Atherosclerotic Cardiovascular Disease in Ancient Human Rem
#1
Genetic Predisposition of Atherosclerotic Cardiovascular Disease in Ancient Human Remains

Abstract

Background: Several computed tomographic studies have shown the presence of atherosclerosis in ancient human remains. However, while it is important to understand the development of atherosclerotic cardiovascular disease (ASCVD), genetic data concerning the prevalence of the disease-associated single nucleotide polymorphisms (SNPs) in our ancestors are scarce.

Objective: For a better understanding of the role of genetics in the evolution of ASCVD, we applied an enrichment capture sequencing approach to mummified human remains from different geographic regions and time periods.

Methods: Twenty-two mummified individuals were analyzed for their genetic predisposition of ASCVD. Next-generation sequencing methods were applied to ancient DNA (aDNA) samples, including a novel enrichment approach specifically designed to capture SNPs associated with ASCVD in genome-wide association studies of modern humans.

Findings: Five out of 22 ancient individuals passed all filter steps for calculating a weighted polygenic risk score (PRS) based on 87 SNPs in 56 genes. PRSs were correlated to scores obtained from contemporary people from around the world and cover their complete range. The genetic results of the ancient individuals reflect their phenotypic results, given that the only two mummies showing calcified atherosclerotic arterial plaques on computed tomography scans are the ones exhibiting the highest calculated PRSs.

Conclusions: These data show that alleles associated with ASCVD have been widespread for at least 5,000 years. Despite some limitations due to the nature of aDNA, our approach has the potential to lead to a better understanding of the interaction between environmental and genetic influences on the development of ASCVD.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10809863/
Riverman, Capsian20, ilabv And 1 others like this post
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#2
Looks like several Egyptian mummies were sampled.

Code:
Australia    Queensland    1904 AD
Switzerland    Basel    The Enlightenment
Italy    Ötztal Alps    Copper Age
Bolivia    Altiplano Region    Late Intermediate Period (1000 - 1470 AD) *
Peru     Area around Lake Titicaca    Late Intermediate Period (1000 - 1470 AD)
Egypt    Unknown    Late Period - Early Ptolemaic (664 BC - 250 BC) *
Egypt    Gebelein    Predynastic, Neqada I (4500 - 3500 BC)
Egypt    Deir el-Bahari (Thebes West)    Byzantine Period (395 - 641 AD)
Egypt    Kom Ombo    Ptolemaic Period (332 - 30 BC) *
Egypt    Unknown    Late Period (664 - 332 BC) - Ptolemaic Period (332 - 30 BC)
Egypt    Unknown    Byzantine Period (395 - 641 AD)
Egypt    Memphis, Abusir    First Intermediate Period (2160 - 2055 BC) - Middle Kingdom (2055 - 1650 BC)
Egypt    Unknown    Third Intermediate Period (1069 - 664 BC)
Egypt    Thebes-West    Roman Period (30 BC - 395 AD) *
Egypt    Akhmim    Third Intermediate Period (106 9− 664 BC) - 21st Dynasty (1069 - 946 BC) *
Egypt    Akhmim    Third Intermediate Period (106 9− 664 BC) - 21st Dynasty (1069 - 946 BC) *
Egypt    Akhmim    Late Period (664 - 332 BC) - Ptolemaic Period (332 - 30 BC)
Egypt    Asyut    Old Kingdom (2686 - 2160 BC) - First Intermediate Period (2160 - 2055 BC)
Egypt    Unknown    Byzantine (Coptic) Period (395 - 641 AD)
Egypt    Unknown    Roman Period (30 BC - 395 AD) - Byzantine Period (395 - 641 AD)
Egypt    Unknown    New Kingdom (1550 - 1069 BC)
Egypt    Unknown    Third Intermediate Period (1069 - 664 BC) - Late Period (664 - 332 BC)
ionix, Riverman, pelop And 2 others like this post
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#3
The Bam & Fastq are available
https://www.ebi.ac.uk/ena/browser/view/PRJEB62880

But it's difficult to extract any useful autosomal SNPs, most likely because the capture process targeted only some specific SNPs associated with atherosclerotic cardiovascular disease (ASCVD)

Quote:Methods: Twenty-two mummified individuals were analyzed for their genetic predisposition of ASCVD. Next-generation sequencing methods were applied to ancient DNA (aDNA) samples, including a novel enrichment approach specifically designed to capture SNPs associated with ASCVD in genome-wide association studies of modern humans.


Most of the Y-chr results of the Egyptian mummies are under R1b (which is questionable)
Capitalis likes this post
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#4
(03-31-2024, 02:29 PM)ionix Wrote: It is difficult to extract any useful autosomal SNPs, most likely because the capture process targeted only some specific SNPs associated with atherosclerotic cardiovascular disease (ASCVD)

Quote:Methods: Twenty-two mummified individuals were analyzed for their genetic predisposition of ASCVD. Next-generation sequencing methods were applied to ancient DNA (aDNA) samples, including a novel enrichment approach specifically designed to capture SNPs associated with ASCVD in genome-wide association studies of modern humans.


Most of the Y-chr results of the Egyptian mummies are under R1b (which is questionable)
Is there the presence of the Chadic R1b in Egypt?
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#5
(03-31-2024, 02:29 PM)ionix Wrote: It's difficult to extract any useful autosomal SNPs, most likely because the capture process targeted only some specific SNPs associated with atherosclerotic cardiovascular disease (ASCVD)

Quote:Methods: Twenty-two mummified individuals were analyzed for their genetic predisposition of ASCVD. Next-generation sequencing methods were applied to ancient DNA (aDNA) samples, including a novel enrichment approach specifically designed to capture SNPs associated with ASCVD in genome-wide association studies of modern humans.


Most of the Y-chr results of the Egyptian mummies are under R1b (which is questionable)

They used shotgun as well.
Qrts, Riverman, ionix like this post
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#6
(03-31-2024, 02:29 PM)ionix Wrote: Most of the Y-chr results of the Egyptian mummies are under R1b (which is questionable)

Old Kingdom Egyptian samples are mostly E-M35 according to reliable leaks both from eurogenes blog/athrogenica the same guy who leaked Etruscans were mostly R1b.
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#7
Aligning them now, will send to Davidski no later than tomorrow. Many are very low quality so keep expectations in check
Ajeje Brazorf, Megalophias, Gabriel90 And 2 others like this post
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#8
(04-01-2024, 01:52 AM)ilabv Wrote: Aligning them now, will send to Davidski no later than tomorrow. Many are very low quality so keep expectations in check

Any idea how long it might take?
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#9
(03-31-2024, 02:29 PM)ionix Wrote: The Bam & Fastq are available
https://www.ebi.ac.uk/ena/browser/view/PRJEB62880

But it's difficult to extract any useful autosomal SNPs, most likely because the capture process targeted only some specific SNPs associated with atherosclerotic cardiovascular disease (ASCVD)

Quote:Methods: Twenty-two mummified individuals were analyzed for their genetic predisposition of ASCVD. Next-generation sequencing methods were applied to ancient DNA (aDNA) samples, including a novel enrichment approach specifically designed to capture SNPs associated with ASCVD in genome-wide association studies of modern humans.


Most of the Y-chr results of the Egyptian mummies are under R1b (which is questionable)

Possibly, are they female?
Capsian20 likes this post
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#10
Apparently they're contaminated European samples?

https://twitter.com/MiroCyo/status/1774967169706860594

What is going on?
Capitalis likes this post
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#11
(04-02-2024, 06:25 PM)James100 Wrote: Apparently they're contaminated European samples?

https://twitter.com/MiroCyo/status/1774967169706860594

What is going on?

this samples its back a era byzantine
Target: CapsianWGS_scaled
Distance: 1.2510% / 0.01251049
37.2 Iberomaurusian
36.8 Early_European_Farmer
12.8 Early_Levantine_Farmer
8.0 Steppe_Pastoralist
4.8 SSA
0.4 Iran_Neolithic
FTDNA : 91% North Africa +<2% Bedouin + <2  Southern-Levantinfo + <1 Sephardic Jewish + 3% Malta +  3%  Iberian Peninsula
23andME :  100% North Africa

WGS ( Y-DNA and mtDNA)
Y-DNA: E-A30032< A30480 ~1610 CE
mtDNA: V25b 800CE ? ( age mtDNA not accurate )
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#12
(04-02-2024, 05:22 PM)Hodo Scariti Wrote:
(03-31-2024, 02:29 PM)ionix Wrote: The Bam & Fastq are available
https://www.ebi.ac.uk/ena/browser/view/PRJEB62880

But it's difficult to extract any useful autosomal SNPs, most likely because the capture process targeted only some specific SNPs associated with atherosclerotic cardiovascular disease (ASCVD)

Quote:Methods: Twenty-two mummified individuals were analyzed for their genetic predisposition of ASCVD. Next-generation sequencing methods were applied to ancient DNA (aDNA) samples, including a novel enrichment approach specifically designed to capture SNPs associated with ASCVD in genome-wide association studies of modern humans.


Most of the Y-chr results of the Egyptian mummies are under R1b (which is questionable)

Possibly, are they female?

very likely they are female , maybe @teepean have info
Target: CapsianWGS_scaled
Distance: 1.2510% / 0.01251049
37.2 Iberomaurusian
36.8 Early_European_Farmer
12.8 Early_Levantine_Farmer
8.0 Steppe_Pastoralist
4.8 SSA
0.4 Iran_Neolithic
FTDNA : 91% North Africa +<2% Bedouin + <2  Southern-Levantinfo + <1 Sephardic Jewish + 3% Malta +  3%  Iberian Peninsula
23andME :  100% North Africa

WGS ( Y-DNA and mtDNA)
Y-DNA: E-A30032< A30480 ~1610 CE
mtDNA: V25b 800CE ? ( age mtDNA not accurate )
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#13
(04-02-2024, 06:59 PM)Capsian20 Wrote:
(04-02-2024, 05:22 PM)Hodo Scariti Wrote:
(03-31-2024, 02:29 PM)ionix Wrote: The Bam & Fastq are available
https://www.ebi.ac.uk/ena/browser/view/PRJEB62880

But it's difficult to extract any useful autosomal SNPs, most likely because the capture process targeted only some specific SNPs associated with atherosclerotic cardiovascular disease (ASCVD)



Most of the Y-chr results of the Egyptian mummies are under R1b (which is questionable)

Possibly, are they female?

very likely they are female , maybe @teepean have info

Supplementary data has info about the sex.
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#14
(04-02-2024, 06:25 PM)James100 Wrote: Apparently they're contaminated European samples?

https://twitter.com/MiroCyo/status/1774967169706860594

What is going on?

Thanks for the laughs:

Quote:Well what do ya know: "The analyses were performed in the ancient DNA Laboratory of the Eurac Research Institute for Mummy Studies–a special DNA Laboratory in Bolzano (Italy)"

They studied themselves. Great job
Known ancestry: 58% English, 36% Irish, 6% Welsh
LivingDNA: 60% English, 32% Irish, 8% Welsh
AncestryDNA communities
MyHeritageDNA genetic groups (LivingDNA upload)
Y-DNA (P): Wiltshire at 10 generations. Negative at YSEQ for all discovered SNPs downstream of R-S15663
mtDNA (M): Co. Cork
mtDNA (P): Co. Limerick
Avatar: My great grandmother at St Mary's Church, St Fagans, circa 1930
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#15
Yes, they are useless. I've posted them somewhere else.

Clearly contaminated, GEDmatch implied so as well.
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