[HTML][HTML] Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

J O'Rawe, T Jiang, G Sun, Y Wu, W Wang, J Hu… - Genome medicine, 2013 - Springer
Background To facilitate the clinical implementation of genomic medicine by next-generation
sequencing, it will be critically important to obtain accurate and consistent variant calls on …

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

G Narzisi, JA O'rawe, I Iossifov, H Fang, Y Lee… - Nature …, 2014 - nature.com
We present an open-source algorithm, Scalpel ( http://scalpel.sourceforge.net/ ), which combines
mapping and assembly for sensitive and specific discovery of insertions and deletions (…

[HTML][HTML] Reducing INDEL calling errors in whole genome and exome sequencing data

H Fang, Y Wu, G Narzisi, JA ORawe, LTJ Barrón… - Genome medicine, 2014 - Springer
… Our validation data showed that with the same X 2 , INDELs with a lower C O Alt tend to …
To achieve a consistent accuracy for INDELs with different C O Alt , we classified INDEL calls …

[PDF][PDF] TAF1 variants are associated with dysmorphic features, intellectual disability, and neurological manifestations

JA O'Rawe, Y Wu, MJ Dörfel, AF Rope, PYB Au… - The American Journal of …, 2015 - cell.com
We describe an X-linked genetic syndrome associated with mutations in TAF1 and
manifesting with global developmental delay, intellectual disability (ID), characteristic facial …

Indel variant analysis of short-read sequencing data with Scalpel

…, K Arora, V Vacic, MC Zody, I Iossifov, JA O'rawe… - Nature protocols, 2016 - nature.com
As the second most common type of variation in the human genome, insertions and deletions
(indels) have been linked to many diseases, but the discovery of indels of more than a few …

Accounting for uncertainty in DNA sequencing data

JA O'Rawe, S Ferson, GJ Lyon - Trends in Genetics, 2015 - cell.com
Science is defined in part by an honest exposition of the uncertainties that arise in
measurements and propagate through calculations and inferences, so that the reliabilities of its …

[HTML][HTML] Natural language of uncertainty: numeric hedge words

S Ferson, J O'Rawe, A Antonenko, J Siegrist… - International Journal of …, 2015 - Elsevier
An important part of processing elicited numerical inputs is an ability to quantitatively decode
natural-language words that are commonly used to express or modify numerical values. …

Human genetics and clinical aspects of neurodevelopmental disorders

GJ Lyon, J O'Rawe - The genetics of neurodevelopmental …, 2015 - Wiley Online Library
This chapter traverses contemporary understandings of the genetic architecture of human
disease, and explores the clinical implications of the current state of knowledge. Many different …

SeqHBase: a big data toolset for family based sequencing data analysis

…, SM Lin, PL Peissig, MH Brilliant, J O'Rawe… - Journal of medical …, 2015 - jmg.bmj.com
Background Whole-genome sequencing (WGS) and whole-exome sequencing (WES)
technologies are increasingly used to identify disease-contributing mutations in human genomic …

[HTML][HTML] Integrating precision medicine in the study and clinical treatment of a severely mentally ill person

JA O'Rawe, H Fang, S Rynearson, R Robison… - PeerJ, 2013 - peerj.com
Background. In recent years, there has been an explosion in the number of technical and
medical diagnostic platforms being developed. This has greatly improved our ability to more …