SNP array analysis

6 Pages
Published On: 6-12-2023

Aim

Analyse and interpret data from SNP array analysis of DNA from a patient, and generate a discussion of SNP array as a diagnostic tool for similar case referrals.

Educational Objectives

After this exercise students should be able to

Understand the principles of SNP array

Interpret results generated from SNP array analysis

Generate an evaluative discussion of SNP array as a diagnostic tool

Introduction

Two different chromosomal microarray approaches have been used in NHS laboratories: initially array genomic hybridisation (aCGH) was used, but aCGH has been superseded by the use of SNP array, which is now a routine first step for many referrals. The West of Scotland Genetics Service currently use Illumina CytoSNP 850K Beadchip.

Case information

Patient details: Alan Mackay; male; date of birth 3/10/2020

Sample details: Peripheral blood

Reason for referral: dysmorphic facies; ventricular septal defect; lamellar cataracts; broncho-pulmonary dysplasia; poorly developed lungs; diastasis recti; diffuse hypotonia; seizures; polymicrogyria with symmetrical cortical malformation and abnormal white matter.

SNP array result

SNP array using Illumina CytoSNP 850K Beadchip: imbalances identified (screenshots follow)

Chromosome 1 p36.33-p36.31

Nucleotide range 82,154 to 8,865,956bp

Note 82,154 is position of tested SNP nearest 1p-terminus

Chromosome 3 q26.33-q29

Nucleotide range 182,373,879 to 197,838,262bp

Note 197,838,262 is position of tested SNP nearest 3q-terminus

Chromosome 9

Further array result views are presented after the assignment instructions below.

Assignment for Data Analysis 2

REPORT PART A (approximately 600-700 words):

Provide an interpretation of the array data making use of resources such as DECIPHER / DGV / UCSC genome browser / OMIM / UNIQUE website (you do not have to use all these resources!) as well as appropriate scientific literature.

Consider whether the array findings correlate with the referral and whether any follow-up may required by the diagnostics laboratory/genetics service. In relation to any suggested follow-up, explain why you think this follow-up is important but do not include extensive discussion of “follow-up for the follow-up” – in other words it is enough to discuss that use of “approach X” might confirm “possibility Y” – you should not use assumptions about the findings from “approach X” as an excuse to write long discussions about “possibility Y”. You may wish to comment briefly on any reported syndromes associated with regions of imbalance in the patient (or particular genes or segments within any of these regions, in which imbalance has been reported to correlate with particular features noted in the patient). Note that follow-up suggestions should be confined to what should be offered by genetics services.

REPORT PART B (approximately 600-700 words):

Provide an evaluative, literature-based review of SNP array as a diagnostic tool in genetic investigation for children with dysmorphology / developmental problems.

General instructions:

Overall word count 1350 ± 10% (or 1500 maximum part A + part B) (word count does not include in-text citations, tables, figure legends, reference list, subheadings)

Figure legends should be no more than 250 words; there is no need to cite sources for the supplied images of array data if used in your report to illustrate any part of your argument – though note that use of these images is not essential to a good report

Use Harvard referencing system

Minimum font size of 12pt should be used for the main text (a minimum font size of 11pt may be used in figure legends and 10pt in references sections).

Minimum line spacing should be 1.2 lines; in the references section a line spacing of 1 line may be used

The word count should be 1350 (with ~10% leeway taking this to 1500, with no penalty imposed on reports ≤1500).