P-746 Carrier Screening analysis in more than 20.000 patients. Is complete analysis important vs genotyping analysis?
Authors: Palahi Bages M , Feliu Cuberes A , Martin Insa A , Moret Turné R , Trujillo Puebla I , Cotán D , Sandalinas Alabert M 
Published: June 2023

Abstract

Study question
How comprehensive gene sequencing analysis impacts on carrier screening (CS) results and couple risk reduction?

Summary answer
Comprehensive genetic sequencing analysis facilitates more accurate carrier rates and provides better information for final panel design and partner risk reduction.

What is known already
Since CS began in the 1970s, it has helped millions of couples at risk of affected offspring affected by genetic diseases.From the first panels for Ashkenazi Jewish to today’s pan-ethnic CS panels, genetic testing has improved from analysis of a few known pathogenic variants to full sequence analysis. The American College of Medical Genetics and Genomics (ACMG) published Standards and Guidelines for the Interpretation of Sequence Variants in 2015, providing an important tool for full sequence analysis for CS. CS analyses can report only already known mutations (genotyping) or screen for all variants with ACMG-guidelines and laboratory experience (full sequencing).

Study design, size, duration
This study includes 20774 patients screened with an expanded carrier screening panel of 301 genes, including autosomal recessive (AR) and X-linked (XL) disorders by next-generation sequencing (NGS). ACMG guidelines for variant interpretation were followed in 13954 patients and only pathogenic and likely pathogenic variants were reported. 6820 patients were analyzed with genotyping analysis. 15758 matching analyses were performed for couples and gamete donors. The study has been conducted between August 2018 and December 2022.

Participants/materials, setting, methods
DNA was extracted from saliva and blood samples and sequenced. The data obtained were processed by means of computer tools. The carrier frequency (CFR) was obtained from the full sequencing analyses. The observed CFRs was compared with the expected CFRs obtained from databases and literature.To define its similarity a range of +-25% was accepted as similar CFR. For matching analyses, high at-risk couples were divided for autosomal recessive diseases(both carriers) and X-linked diseases (female carriers).

Main results and the role of chance
For the 301 genes analyzed, 34%(103) had a similar CF than the expected one and, more importantly, 65%(198) showed different CFR. In some cases this difference is due to the lack of complete information on the CFR on bibliography and databases like the CFR associated a diseases with more than one gene associated or genes related with more than one disease, some of which with low clinical implications, usually underdiagnosed. One of the genes on which the CFR was not similar to the expected was SMN1. For this well-known gene, related to spinal muscular atrophy, the CFR was higher than expected, probably due to the analysis of the variants c.*3 + 80T&gt;G(p.?),c.*211_*212del(p.?) that indicate a higher risk of 0 + 2 configuration. The patients with these variants and 2 SMN1-exon8 copies are at higher risk to be silent carriers, but they may not be carriers.
For the 15758 performed, if one or both patients were analyzed by genotyping analysis, 3,6% (432/12055 matchings) identified had high risk of affected offspring for autosomal or X-Linked recessive diseases. When both patients were analyzed by sequencing, 6% (223/3703 matchings) were identified at high risk of affected offspring of the diseases analyzed allowing a higher identification of couples at risk.

Limitations, reasons for caution
The analysis was performed on 301 genes, in order to have a better understanding of CFR for panel designs or patients genetic counseling, a larger cohort of genes should be taken into account, these results show the importance of complete analysis to assess the carrier risks.

Wider implications of the findings
It is important to have wider genetic databases for CFR but also for variant pathogenicity in order to have better results on CFR analyses and panel designs, in order to provide proper genetic counseling to patients looking to improve the chances of healthy offspring.

Trial registration number
Not applicable