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Non-LTR Retrotransposons

Non-LTR Retrotransposons

As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...

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Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

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Mobile element insertion detection in 89,874 clinical exomes.

Rebecca I Torene¹, Kevin Galens², Shuxi Liu²

¹GeneDx, Gaithersburg, MD, USA. rtorene@genedx.com.

Genetics in Medicine : Official Journal of the American College of Medical Genetics

|January 23, 2020

Summary

This summary is machine-generated.

A new method for detecting mobile element insertions (MEIs) using exome sequencing (ES) improves rare genetic disease diagnosis. This approach increases diagnostic yield by 0.15%, identifying variants missed by other assays.

Keywords:

Mendelian disease diagnostics exome sequencing mobile elements rare disease

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Area of Science:

Genomics
Human Genetics
Molecular Diagnostics

Background:

Exome sequencing (ES) is vital for diagnosing rare genetic diseases.
Pathogenic sequence variants can be missed by standard ES.
Mobile element insertions (MEIs) are a known cause of genetic disease but are difficult to detect with current sequencing methods.

Purpose of the Study:

To develop and apply a novel method for detecting MEIs from exome sequencing data.
To assess the diagnostic utility of MEI detection in a clinical setting.
To determine the impact of MEI detection on the overall diagnostic yield for rare genetic diseases.

Main Methods:

A novel MEI detection method was developed and prospectively applied to clinical ES samples.
Positive MEI findings were confirmed using an orthogonal method.
The study analyzed 89,874 samples from 38,871 cases.

Main Results:

Diagnostic MEIs were identified in 0.03% of all cases and 0.15% of cases with a molecular diagnosis.
One diagnostic MEI represented a novel founder event.
Most patients with pathogenic MEIs had prior genetic testing, including some with negative DNA sequencing results for the diagnostic gene.

Conclusions:

MEI detection from ES is a valuable diagnostic tool for rare genetic diseases.
This method identifies molecular findings that may be missed by other sequencing assays.
MEI detection increases the diagnostic yield of exome sequencing by 0.15%.