Thursday, January 28, 2016

DNA Land Results

I took my AncestryDNA data and uploaded it to The results were quite consistent with AncestryDNA and Genes For Good, although the focus is on regions rather than individual countries. They do provide a nice summary figures.

Friday, January 15, 2016

Puerto Rico is the ultimate melting pot: Ancestry DNA results

I just received my Ancestry DNA results. Wow, Puerto Rico is a serious melting pot, I had no idea of the multitude of sources for my ancestry. The results are quite consistent with Genes For Good, but with more detail. The main discrepancy is based on classification differences, Genes For Good puts North African together with West Asian, while AncestryDNA puts North African with African, hence my % African is higher in Ancestry DNA.

66% European
7% West Asian
15% African
11% Native American

Here is a bar chart of the details, excluding contributions below 1% (South Asian, South African).

Wednesday, January 6, 2016

Accepted at Genome Research: Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations

Below is the abstract of an article that answers the fundamental question "Where did Arabs come from?". By sequencing the genomes of 108 Qataris, including 60 of indigenous Arab/Bedouin ancestry, our study begins to answer the question. Full text available here.

Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations
Genome Research, Online access January 4, 2015

An open question in the history of human migration is the identity of the earliest Eurasian populations that have left contemporary descendants. The Arabian Peninsula was the initial site of the out of Africa migrations that occurred between 125,000 - 60,000 years ago, leading to the hypothesis that the first Eurasian populations were established on the Peninsula and that contemporary indigenous Arabs are direct descendants of these ancient peoples. To assess this hypothesis, we sequenced the entire genomes of 104 unrelated natives of the Arabian Peninsula at high coverage, including 56 of indigenous Arab ancestry. The indigenous Arab genomes defined a cluster distinct from other ancestral groups and these genomes showed clear hallmarks of an ancient out of Africa bottleneck. Similar to other Middle Eastern populations, the indigenous Arabs had higher levels of Neanderthal admixture compared to Africans but had lower levels than Europeans and Asians. These levels of Neanderthal admixture are consistent with an early divergence of Arab ancestors after the out of Africa bottleneck but before the major Neanderthal ad-mixture events in Europe and other regions of Eurasia. When compared to worldwide populations sampled in the 1000 Genomes Project, while the indigenous Arabs had a signal of admixture with Europeans, they clustered in a basal, outgroup position to all 1000 Genomes non-Africans when considering pairwise similarity across the entire genome. These results place indigenous Arabs as the most distant relatives of all other contemporary non-Africans and identify these people as direct descendants of the first Eurasian populations established by the out of Africa migrations.

Wednesday, December 9, 2015

Genes for Good Ancestry Results

Today I logged into Facebook and got some exciting news, my saliva DNA sample was analyzed by Genes for Good, and they sent me results on ancestry analysis. They sent me three slides, including (A) a pie chart with my proportion of ancestry from different sources, (B) A representation of my maternal/paternal chromosomes, showing large chunks of DNA specific to each ancestry, and (C) where my genome lies in a spectrum of globally sampled genomes.

The results are quite interesting. My Native American and Sub-Saharan African ancestry are in line with what is expected for Puerto Ricans. According to family legend, most of my ancestors came from Mediterranean Europe (Spain and Italy) in the 18th century, hence the 61% European ancestry is to be expected. I'm curious as to what the 17% West Asia and North Africa ancestry means. 

A. Summary of my ancestry mixture.
B. Chromosomal fragments of specific ancestry. I can't wait to get my hands on the data, to see my ancestry for different genes. Also, my parents recently signed up for AncestryDNA, it would be very interesting to see what I got from each parent. It looks like the Native American and Sub-Saharan ancestry are on the same chromosome, a truly Puerto Rican mix!
 C. Where does my genome lie in comparison to other populations? There I am, right in the middle, a bit more African than Europeans (PC1) and a bit more African than Europeans (PC2). This method collapses millions of dimensions of genetic variation into a 2D image, not exactly the most accurate result, it does not make sense that I am overlapping with Central and South Asian populations.
 Overall and interesting result, I'd highly recommend signing up for Genes For Good to anyone.

Friday, November 20, 2015

My Genome

A few years ago my genome and microbiome was sequenced by the Personal Genome Project. If anyone is interested, here is a link to the data.

Tuesday, January 7, 2014

In print: Exome Sequencing Identifies Potential Risk Variants for Mendelian Disorders at High Prevalence in Qatar

Just published in Human Mutationour second article on disease risk allele prevalence in Qatar.

This study presents a framework for enabling precision genome-based medicine (PGM) in a population not sampled by nor related to public consortium sequencing projects, using the example of Qatar. Through sampling and exome sequencing of representatives from three major ancestry groups identified in prior work (Q1 Bedouin, Q2 Persian-South Asian, Q3 African), we identified 37 variants in 33 genes with effects on 36 clinically significant Mendelian diseases. Genetic screening in Qatar includes only 4 out of the 37. This study provides a set of Mendelian disease variants with potential impact on the epidemiological profile of the population that could be incorporated into the testing program if further experimental and clinical characterization confirms high penetrance.

Wednesday, March 20, 2013

My first paper as lead author at Cornell: Exome Sequencing of Only Seven Qataris Identifies Potentially Deleterious Variants in the Qatari Population

The Qatari population, located at the Arabian migration crossroads of African and Eurasia, is comprised of Bedouin, Persian and African genetic subgroups. By deep exome sequencing of only 7 Qataris, including individuals in each subgroup, we identified 2,750 nonsynonymous SNPs predicted to be deleterious, many of which are linked to human health, or are in genes linked to human health. Many of these SNPs were at significantly elevated deleterious allele frequency in Qataris compared to other populations worldwide. Despite the small sample size, SNP allele frequency was highly correlated with a larger Qatari sample. Together, the data demonstrate that exome sequencing of only a small number of individuals can reveal genetic variations with potential health consequences in understudied populations. Full Text