The Need for Realignment to dbSNP

We’ve been using Avadis NGS to analyze a number of clinical samples and ran into an interesting case for InDel detection that could lead to false interpretation unless handled properly. The case at hand involves a child who suffered from Pulmonary Hypertension, Pulmonary Infections, and a few other abnormalities, all at birth or in the … Continue reading “The Need for Realignment to dbSNP”

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Benford’s Law and NGS Gene Counts

This may be a piece of trivia more than anything else, but anyway, let’s begin with the surprising part. Take any RNASeq sample and assign to each gene a count corresponding to the number of reads aligning to that gene (what we call Quantification in Avadis NGS). For the purposes of this post, ignore all … Continue reading “Benford’s Law and NGS Gene Counts”

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Mutations Causing CHIME Disease

Here is publication from Sanford-Burnham Medical Research Institute that uses Avadis NGS: http://www.sciencedirect.com/science/article/pii/S000292971200095X The goal in this paper is to find the underlying genomic cause of CHIME syndrome, a disease so rare that there are only 8 reported cases in the world. CHIME is an abbreviation derived from the main symptoms: Colobomas (hole in the … Continue reading “Mutations Causing CHIME Disease”

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RNA-Seq Analysis of Functional Compartments in the Rat Placentation Site

We just read a recent publication by Shankar et al that uses Avadis NGS to analyze RNA-Seq data. They study cells involved in rat placenta formation. The placenta is an organ that connects the foetus to the wall of the uterus, thus allowing for nutrients/oxygen to flow from mother to foetus, and waste to flow … Continue reading “RNA-Seq Analysis of Functional Compartments in the Rat Placentation Site”

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Diagnosing a Neuro-muscular Disorder

We just read a recent publication that used Avadis NGS in the process of diagnosing the case of a Japanese boy suffering from a neuromuscular disorder. Here is a link to the paper. The case is summarized below: The boy was born in a family with no history of neuromuscular disease. He experienced transient breath-holding … Continue reading “Diagnosing a Neuro-muscular Disorder”

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Genes That Smell

The Lab for Neurogenetics and Behavior at Rockefeller University has an ongoing Smell Study that states: Given almost any odor, some people will find it pleasant, others unpleasant. Ripe cheese or garlic may smell delicious to some, but repulsive to others. The scientific basis of this variation has not been well-studied. Despite the clear evidence … Continue reading “Genes That Smell”

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How Identical are Identical Twins?

We’re looking at exome sequencing data on whole peripheral blood DNA of monozygotic twins (this data was generated by our collaborators, Jan Dumanskiand his group at Uppsala University in Sweden). Monozygotic twins were earlier thought to be genetically identical; now we know that isn’t completely true. How does one identify small mutations (SNPs and small … Continue reading “How Identical are Identical Twins?”

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