identical twin 5.2 SNP

 

https://www.newser.com/story/301012/identical-twins-not-as-identical-as-we-thought.html

"On average, identical twins have 5.2 of these early genetic differences, the researchers found. But about 15% of identical twin pairs have more genetic differences, some of them up to 100, said Stefansson"

Thalassemia

Thalassemia module References

https://en.wikipedia.org/wiki/Thalassemia

http://www.healthline.com/health/thalassemia#Symptoms3

http://www.ncbi.nlm.nih.gov/pubmed/22445352

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656091/pdf/ppat.1003327.pdf

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666573/pdf/ejhg2014131a.pdf

homo sapiens migration

https://www.facebook.com/businessinsider/videos/vb.20446254070/10152823614039071/?type=2&theater

PCA, snp matrix, human population

For human snp in maxtrix

                  site1   site2
people1      0          1...
people2      2          0 ...

0: aa, 1 Aa, 2 AA

So, PCA can be calculated from this matrix pretty straightfoward.

Ref
https://www.youtube.com/watch?v=SlnOxHhypDg

admixture mapping

admixture mapping
two ancestral population

https://www.youtube.com/watch?v=syKWlFjzUss

https://www.youtube.com/watch?v=zGha8i8Xzpk

CNV and network analysis references, human diseases

PubMed ID: 24244640;
CNVannotator: a comprehensive annotation server for copy number variation in the human genome.

PMID:22729399 for PPI;
Proteome-wide prediction of protein-protein interactions from high-throughput data.

PMID:24067414 for gene network,
Gaussian graphical model for identifying significantly responsive regulatory networks from time course high-throughput data.

PMID:22360268 for network-based disease analysis; and
Network-based analysis of complex diseases.

PMID:14735121 for network biology
Network biology: understanding the cell's functional organization.

20150718:
http://www.nature.com/nature/journal/v464/n7289/abs/nature08979.html
Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

http://www.nature.com/nature/journal/v464/n7289/abs/nature08516.html
Origins and functional impact of copy number variation in the human genome

CNV basics, human, African American, McElroy 2009

McElroy 2009 BMC Genetics

3.5 CNV per individual in African Americans
4.8 CNV per individual in white (a bit inflated due to the reference)
when the reference is a pool of 50 randomly chosen AA women were used as references.

Except two CNV (one on chr17 and one on chr15), all other CNVs vary within 10% between African American and Caucasians.