A multi-sample based method for identifying common CNVs in normal human genomic structure using high-resolution aCGH data

MSeq-CNV: accurate detection of Copy Number Variation from Sequencing of Multiple samples

Currently a few tools are capable of detecting genome-wide Copy Number Variations (CNVs) based on sequencing of multiple samples. Although aberrations in mate pair insertion sizes provide additional hints for the CNV detection based on multiple samples, the majority of the current tools rely only on the depth of coverage. Here, we propose a new algorithm (MSeq-CNV) which allows detecting common CNVs across multiple samples. MSeq-CNV applies a mixture density for modeling aberrations in depth of coverage and abnormalities in the mate pair insertion sizes. Each component in this mixture density applies a Binomial distribution for modeling the number of mate pairs with aberration in the insertion size and also a Poisson distribution for emitting the read counts, in each genomic position. MSeq-CNV is applied on simulated data and also on real data of six HapMap individuals with high-coverage sequencing, in 1000 Genomes Project. These individuals include a CEU trio of European ancestry and a YRI trio of Nigerian ethnicity. Ancestry of these individuals is studied by clustering the identified CNVs. MSeq-CNV is also applied for detecting CNVs in two samples with low-coverage sequencing in 1000 Genomes Project and six samples form the Simons Genome Diversity Project.

Best practices of ASRM and ESHRE: a journey through reproductive medicine

BACKGROUND

The American Society for Reproductive Medicine (ASRM) and the European Society of Human Reproduction and Embryology (ESHRE) are the two largest societies in the world whose members comprise the major experts and professionals working in the field of reproductive medicine and embryology. These societies have never before had a joint scientific meeting.

METHOD(S)

A 3-day meeting was planned and took place in March of 2012. The goal was to present and debate key topics, as well as modes of practice in reproductive medicine and to discuss recent developments in the field.

RESULT(S)

Presentations by members of ASRM and ESHRE were of three types: 'state of the art' lectures, 'back-to-back' presentations of two points of view and debates.

CONCLUSION(S)

For the first time, ASRM and ESHRE held a joint meeting where a special emphasis was given to presentations on the hottest topics in the field. Although different opinions and approaches sometimes exist on the two sides of the Atlantic, an appreciation and acceptance of these differences was evident, and there was more commonality than divergence of opinion.

Best practices of ASRM and ESHRE: a journey through reproductive medicine

BACKGROUND

The American Society for Reproductive Medicine (ASRM) and the European Society of Human Reproduction and Embryology (ESHRE) are the two largest societies in the world whose members comprise the major experts and professionals working in the field of reproductive medicine and embryology. These societies have never before had a joint scientific meeting.

METHODS

A 3-day meeting was planned and took place in March of 2012. The goal was to present and debate key topics, as well as modes of practice in reproductive medicine and to discuss recent developments in the field.

RESULTS

Presentations by members of ASRM and ESHRE were of three types: 'state of the art' lectures, 'back-to-back' presentations of two points of view and debates.

CONCLUSIONS

For the first time, ASRM and ESHRE held a joint meeting where a special emphasis was given to presentations on the hottest topics in the field. Although different opinions and approaches sometimes exist on the two sides of the Atlantic, an appreciation and acceptance of these differences was evident, and there was more commonality than divergence of opinion.