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/
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)
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)
(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?
(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.
(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.
Aligning them now, will send to Davidski no later than tomorrow. Many are very low quality so keep expectations in check
(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?
(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?
(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
have info
(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 have info
Supplementary data has info about the sex.
Yes, they are useless. I've posted them somewhere else.
Clearly contaminated, GEDmatch implied so as well.