Automated copy number variation concordance analysis

Rapid growth and advancement of next generation sequencing (NGS) technologies have changed the landscape of genomic medicine. Today, clinical laboratories perform DNA sequencing on a regular basis, which is an error prone process. Erroneous data affects downstream analysis and produces fallacious result. Therefore, external quality assessment (EQA) of laboratories working with NGS data is crucial. Validation of variations such as single nucleotide polymor- phism (SNP) and InDels (<50 bp) is fairly accurate these days. However, detection and quality assessment of large changes such as the copy number variation (CNV) continues to be a concern. In this work, we aimed to study the feasibility of an automated CNV concordance analysis for the laboratory EQA services. We benchmarked variants reported by 25 laboratories against the highly curated gold standard for the son (HG002/NA24385) of the askenazim trio from the Personal Genome Project published by the Genome in a Bottle Consortium (GIAB). We employed two methods to conduct concordance of CNVs, the sequence based comparison with Truvari and the in-house exome-based comparison. For deletion calls of two whole genome sequencing (WGS) submissions, Truvari gained a value greater than 88% and 68% for precision and recall respectively. Conversely, the in-house method’s precision and recall score peaked at 39% and 7.9% respectively for one WGS submission for both deletion and duplication calls. The results indicate that automated CNV concordance analysis of the deletion calls for the WGS-based callset might be feasible with Truvari. On the other hand, results for panel-based targeted sequencing for the deletion calls showed precision and recall rates ranging from 0-80% and 0-5.6% respectively with Truvari. The result suggests that automated concordance analysis of CNVs for targeted sequencing remains a challenge. In conclusion, CNV concordance analysis depends on how the sequence data is generated

Software Development Process in Small Enterprises : An insight into distributed development

The aim of this study is to analyse the overall work flow and processes that takes place in small enterprises during software development and give an insight into the distributed approach in software development. There are thousands of small sized software companies all around the world. Naturally, small firms possess fewer resources and manpower than bigger companies like Microsoft and Oracle. However, the contributions made by these firms to the software industry are outstanding. The world has turned into a global village. Information Technology is the father of this remarkable achievement of mankind. Hence, it is obvious that this field benefits the most from it. One of the advantages is that the software development can be distributed in various geographical locations, which is a huge leap from the traditional development methods. The possibility of distribution of development team has given a birth to a new kind of era, which is known as software outsourcing. Outsourcing is a very effective method to employ for rapid and creative development. In fact, it provides huge financial savings to businesses. Nevertheless, outsourcing also creates problems, which are irrelevant in centralized development. Those probable problems should be considered beforehand or it will jeopardize the entire project