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  Pseudocholinesterase deficiency
Posted by: tipirneni - 8 hours ago - Forum: Medical Genetics - No Replies

Pseudocholinesterase deficiency is a condition that results in increased sensitivity to certain muscle relaxant drugs used during general anesthesia, called choline esters. These fast-acting drugs, such as succinylcholine and mivacurium, are given to relax the muscles used for movement (skeletal muscles), including the muscles involved in breathing. The drugs are often employed for brief surgical procedures or in emergencies when a breathing tube must be inserted quickly. Normally, these drugs are broken down (metabolized) by the body within a few minutes of being administered, at which time the muscles can move again. However, people with pseudocholinesterase deficiency may not be able to move or breathe on their own for a few hours after the drugs are administered. Affected individuals must be supported with a machine to help them breathe (mechanical ventilation) until the drugs are cleared from the body.
People with pseudocholinesterase deficiency may also have increased sensitivity to certain other drugs, including the local anesthetic procaine, and to specific agricultural pesticides. The condition causes no other signs or symptoms and is usually not discovered until an abnormal drug reaction occurs.

from  Pseudocholinesterase deficiency: MedlinePlus Genetics

Genetic variants in the BCHE (butyrylcholinesterase) gene are associated with reduced BChE enzyme activity and prolonged post-succinylcholine neuromuscular blockade, which can lead to postanesthetic apnea and respiratory depression. 

BCHE variants in a cohort of 13,301 patients of different ethnicities from all 50 states in US shows BCHE reduced function variants in all four major ethnicities in the US. Indeed, this is the first study reporting BCHE variant frequencies in African-Americans and Hispanics. Among the 4 ethnic groups, Caucasians were found to have the highest frequency of individuals who were positive for at least one variant with severely reduced function (A, F1, F2 and/or S1). Accordingly, Caucasians had the highest frequency of predicted moderate and severe BChE deficiency, followed by Hispanics. It is tempting to speculate that African-Americans and Asians may have lower risk of prolonged neuromuscular blockade by succinylcholine. However, it is also possible that other genetic variants may be important in determining BChE activity in these ethnic groups.  from BCHE study

Frequencies of Predicted BChE Phenotype Categories in Different Ethnic Groups

                               Total               African-American           Asian                  Caucasian                Hispanic
                               N Freq            N Freq                          N Freq                N Freq                     N Freq
Normal BChE activity  8402 0.6317   594 0.665     43 0.74       3754 0.6228      221 0.737
Mild BChE deficiency  3816 0.2869   252 0.282     13 0.22       1726 0.2863      61 0.203
Moderate BChE def 1075 0.0808  47 0.053      2 0.03        547 0.0907       18 0.060
Severe BChE def   8 0.0006        0 0        0 0           1 0.0002         0 0
Total             13301            893       58            6028             300


Alaskan Inuit have unusually high gene frequency for PCE deficiency. A relatively high frequency also was reported among Jews from Iran and Iraq, Caucasians from North America, Great Britain, Portugal, Yugoslavia, and Greece. 

Multiple studies done both in and outside India have shown an increased prevalence of pseudocholinesterase deficiency amongst the Arya Vysya community. A study performed in the Indian state of Tamil Nadu in Coimbatore on 22 men and women from this community showed that 9 of them had pseudocholinesterase deficiency, which translates to a prevalence that is 4000-fold higher than that in European and American populations. Vysyas from the South Indian state of Telengana and Andhra were also100-fold higher rate of butyrylcholinesterase deficiency among them and also 50% mortality rate for coronavirus probably due to other conditions. They have one of the highest endogamy rates within subgroup for past few thousand years.

https://www.thehansindia.com/andhra-pradesh/nellore-vysyas-highly-vulnerable-to-coronavirus-685441

Pseudocholinesterase deficiency is common within the Persian and Iraqi Jewish populations. Approximately one in 10 Persian Jews are known to have a mutation in the gene causing this disorder and thus one in 100 couples will both carry the mutant gene and each of their children will have a 25% chance of having two mutant genes, and thus be affected with this disorder. This means that one out of 400 Persian Jews is affected with this condition

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  Share your results for Moderns Only (sims included)from Moriopoulos 2024 update
Posted by: Mulay 'Abdullah - Yesterday, 08:34 PM - Forum: Autosomal (auDNA) - Replies (2)

Hello all, the link for to download the coordinates are here:
G25-All Valentine's Day Averages Moderns Only.txt - Google Drive

2 Way, link:
https://output.jsbin.com/gojecoh

[Image: Capture-d-cran-2024-02-23-175536.png]

[Image: Capture-d-cran-2024-02-23-180148.png]

[Image: Capture-d-cran-2024-02-23-180252.png]

[Image: Capture-d-cran-2024-02-23-180404.png]

[Image: Capture-d-cran-2024-02-23-175850.png]




Chebyshev distance, link:
https://vahaduo.github.io/chebyshev/

[Image: Capture-d-cran-2024-02-23-180452.png]

[Image: Capture-d-cran-2024-02-23-180556.png]

[Image: Capture-d-cran-2024-02-23-180656.png]

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  The first maternal genetic study of hunter-gatherers from Vietnam
Posted by: crashdoc - Yesterday, 08:14 PM - Forum: Ancient (aDNA) - Replies (2)

Abstract
The current limitation of ancient DNA data from Vietnam led to the controversy surrounding the prehistory of people in this region. The combination of high heat and humidity damaged ancient bones that challenged the study of human evolution, especially when using DNA as study materials. So far, only 4 k years of history have been recorded despite the 65 k years of history of anatomically modern human occupations in Vietnam. Here we report, to our knowledge, the oldest mitogenomes of two hunter-gatherers from Vietnam. We extracted DNA from the femurs of two individuals aged 6.2 k cal BP from the Con Co Ngua (CCN) site in Thanh Hoa, Vietnam. This archeological site is the largest cemetery of the hunter-gatherer population in Southeast Asia (SEA) that was discovered, but their genetics have not been explored until the present. We indicated that the CCN haplotype belongs to a rare haplogroup that was not detected in any present-day Vietnamese individuals. Further matrilineal analysis on CCN mitogenomes showed a close relationship with ancient farmers and present-day populations in SEA. The mitogenomes of hunter-gatherers from Vietnam debate the “two layers” model of peopling history in SEA and provide an alternative solution for studying challenging ancient human samples from Vietnam.

Published: 12 July 2023

https://link.springer.com/article/10.100...23-02050-0

In the article they make much of the R0 haplogroup of the two hunter gatherers (CCN24 & CCN55) and they also place them in a mtdna tree that they generated.

I have created this thread as a warning for those who would blinding take what they say for cash.

First, their mtdna tree is garbage, not properly rooted and as a results, recurrent snps make a mess of it.

Second, as you can see in the supplementaries https://static-content.springer.com/esm/...3_ESM.xlsx , both individuals are contaminated.

We can also see the details of their haplogrep that gave an R0 result.

Haplogrep works by finding the best matching line away from rCRS (H2a2a1), see for instance: https://haplogrep.i-med.ac.at/phylogenie...ogroups/R9

As a result of contamination from an M8 (probably C) line the real R9 result gets lost because both lines fight away from each other starting from R towards M8 (maybe C) and the other branch towards R9 (maybe R9c1b1).

The first thing that catches the eye is that they both have 73G, so they definitely can't be R0.

Then among the others snps, we can discern 2 lines, one from the actual hunter gatherers and the other presumably from the modern individual dna from whom the samples are contaminated:

73G -> out of R0 (both have it)

14783C -> M (both have it)
4715G -> M8 (CCN24 so both have 1 M8 defining snp)
7196A -> M8 (CCN55 so both have 1 M8 defining snp)
14318C -> C (which is below M8, CCN55)
16209C -> C1d2a (CCN55) was there a Columbian man on the extraction team? Or maybe coincidence as with other recurrent snps that I have not shown.

13928C -> R9 (both have it)
7684C -> R9c1b1 (CCN55)

On yfull mtree R9c1b1 has a TMRCA of 8900ya and is present in Vietnam & Thailand.

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  Why the discrepancy in the % of arab admixture i have on G25 vs qpAdm?
Posted by: abceff - Yesterday, 02:21 PM - Forum: Autosomal (auDNA) - Replies (1)

should i model myself on G25 without a levantine source (potential overfit with arabian even though it is real), i am around 10-11% arab

Code:
Target: abceff_scaled
Distance: 2.0176% / 0.02017645
52.6    TUN_Kerkouane_IA
29.4    Aegean/Anatolian(780–30BC)
11.8    Arab_Modern
6.2    Yoruba
which, makes sense given my family history (maternally arab). though, when i run myself on qpAdm, the arab source is totally rejected:

failed model with bedouinB/higher SE than weight

Code:
> results$weights
# A tibble: 4 × 5
  target left                            weight     se     z
  <chr>  <chr>                            <dbl>  <dbl> <dbl>
1 abceff Mozabite.DG                     0.614  0.0716 8.58
2 abceff Congo_NgongoMbata_Protohistoric 0.0612 0.0164 3.74
3 abceff BedouinB.DG                     0.0897 0.182  0.493
4 abceff Turkey_Hellenistic              0.235  0.128  1.83
> results$popdrop$p[1]
[1] 0.007519254

passing model, with no arabian population in left

Code:
> results$weights
# A tibble: 3 × 5
  target left                            weight     se     z
  <chr>  <chr>                            <dbl>  <dbl> <dbl>
1 abceff Mozabite.DG                     0.622  0.0498 12.5
2 abceff Congo_NgongoMbata_Protohistoric 0.0634 0.0150  4.22
3 abceff Turkey_Byzantine                0.315  0.0391  8.05
> results$popdrop$p[1]
[1] 0.0534153

the model which works best for me so far is a two way r10667 + SSA one

Code:
> results$weights
# A tibble: 2 × 5
  target left                            weight     se     z
  <chr>  <chr>                            <dbl>  <dbl> <dbl>
1 abceff R10667_Nafrican_Outlier_Austria 0.936  0.0150 62.5
2 abceff Congo_NgongoMbata_Protohistoric 0.0640 0.0150  4.27
> results$popdrop$p[1]
[1] 0.1265692

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  Benghazi Y-DNA chart i made using the data from elmrighni et al + libyaftdna project
Posted by: abceff - Yesterday, 01:41 PM - Forum: Northern - Replies (1)

I ran all the STR (values? not sure what they are called lol) through the nevgen y haplo predictor + verified a few of the libyans on the ftdna projects' eastern origins, either through last name or from the city they originate from. not sure how to upload images onto here, so feel free to message me for more info regarding anything.

https://imgur.com/a/jxaioio

for those who don't click the link, the results read:

31% E-M81
29.1% J1
14.8% J2
3.9% T
3% R1B-V88 
2% E-M35
2% R1B-M269
1.5 % Q
5.4% E-M2

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  Nowhere Man: R1b-FT360002
Posted by: rmstevens2 - 02-22-2024, 11:58 PM - Forum: R-PF6323 - Replies (3)

Here is my R1b-PF6323 Descendant Tree again so that you can see where FT360002 is. It has two descendant branches, FT360000 and FTA35718, and that's it. That's where things stop. Apparently, as far as we know, both of those lines are extinct and, thus, so is FT360002 as a whole.

[Image: R1b-PF6323-Descendant-Tree.jpg]

When you go to R-FT360002 in FTDNA Discover and click on Country Frequency, you get "No frequency data available for this haplogroup." So, evidently, as far as FTDNA's team knows, there are no modern descendants of R-FT360002.

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  Haplogroup D1 Discussion Thread
Posted by: alchemist223 - 02-22-2024, 05:11 PM - Forum: D - Replies (2)

Do not belong to this haplogroup myself, but I am interested in it as it is one of the major maternal haplogroups the took part in the peopling of the Americas over 15,000 years ago. Also interested regarding its place among maternal Haplogroup D; it appears to be an independent branch (with no closely related branches) of Haplogroup D4, which otherwise is mostly found in East Asian populations (though not SE Asia).

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  Haplogroup B2 Discussion Thread
Posted by: alchemist223 - 02-22-2024, 05:10 PM - Forum: B - No Replies

Do not belong to this haplogroup myself, but I am interested in it as it is one of the major maternal haplogroups the took part in the peopling of the Americas over 15,000 years ago. Also interested regarding its place among maternal Haplogroup B; it specifically belongs to branch Haplogroup B4b and is most closely related to Haplogroup B4b1, which is found in modern-day East Asian populations.

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  Haplogroup A2 Discussion Thread
Posted by: alchemist223 - 02-22-2024, 05:09 PM - Forum: A - Replies (5)

Do not belong to this haplogroup myself, but I am interested in it as it is one of the major maternal haplogroups the took part in the peopling of the Americas over 15,000 years ago (as well as its presence in some indigenous Siberian ethnic groups). Also interested regarding its place among maternal Haplogroup A; it belongs to the derived A-a and A-a1 subclades of Haplogroup A, along with some other branches of that haplogroup.

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  Question About AR33K Sample?
Posted by: alchemist223 - 02-22-2024, 11:16 AM - Forum: Ancient (aDNA) - Replies (5)

I am curious about the (alleged) Y-DNA chromosomal haplogroup of the AR33K sample from the paper "The deep population history of northern East Asia, which comes from Paleolithic-era China. Some online sources say the sample has belonged to Y-Chromosomal haplogroup P-P226, but for some reason I seem to recall that the sample was actually a female and belonged to mtDNA haplogroup B (just like the Tianyuan sample). 

Does anyone know what information is correct?

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