Article

Linking Genomics and Medical Research Labs

Blog Staff


07-Jan-2019


What’s the connection between conservation of great apes, origin and genetic diversity of Indian population, and genetic variants in human disease? Well, the common thread between these seemingly diverse subjects is that they were all studied by one core facility in Barcelona. The Genomics Core Facility at the Universitat Pompeu Fabra (UPF) is engaged in several collaborative research projects with labs at the Experimental and Health Sciences Department at UPF and develops its own projects focused on new method development for NGS applications. The necessity to develop innovative methods is important when working with degraded and noninvasive samples, material obtained from rare disease conditions, small RNA or single cells. The facility’s chair, Dr. Ferran Casals, a long-term user of Roche NGS sample preparation and PCR products, acts as a link between genomics and medical labs, enabling them to reach their goals. Read about one of their many diverse research projects.

Analyzing whole-exome and genome sequences to understand genetic diversity of Indian populations

The Indian population is known for its complex genetic composition.1 Dr. Casals and collaborators have focused part of their research on unraveling the genetic diversity and origin of this population. In 2014 they published a study based on whole-exome sequencing using the SeqCap EZ probes in one North and one South Indian population2 for detecting an excess of private genetic variation and for showing the need of extending human genetic variation screenings to new populations. Next, in a study published in Nature Genetics,3 they analyzed whole-genome sequences of 10 Andamanese and 60 mainland populations and derived three important findings:  the existence of a single out of Africa genetic event for all Asian and Pacific populations, the presence of genetic contribution from an extinct unknown hominin, and the action of natural selection having produced short stature in Andamanese. Later, in a new study published in Human Genetics4 they performed ancestry analyses utilizing the Y-chromosome sequences, as it does not normally recombine and makes reconstruction of haplotypes easier.  The phylogeny data demystified the North-South genetic divide and revealed almost similar origins for both populations. It also uncovered the possibility of an ancient shared ancestry between Indian population and Southern-European populations. Their final analysis suggested that Indian populations have complex ancestry which cannot be explained by a single expansion model. 

Learn more about Dr. Casals research and team.

 

References

  1. Basu et al. PNAS 2015;113:201513197.
  2. Juyal at al. Hum Genet 2014; 133:201513197
  3. Mondal et al. Nature Genetics 2016 48(9): 1066-70
  4. Mondal et al. Hum Genet.2017;136:499-510

 

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