Genomic testing in 1019 individuals from 349 Pakistani families results in high diagnostic yield and clinical utility

Abstract

We implemented a collaborative diagnostic program in Lahore (Pakistan) aiming to establish the genetic diagnosis, and to asses diagnostic yield and clinical impact in patients with suspected genetic diseases. Local physicians ascertained pediatric patients who had no previous access to genetic testing. More than 1586 genetic tests were performed in 1019 individuals (349 index cases, 670 relatives). Most frequently performed tests were exome/genome sequencing (ES/GS, 284/78 index cases) and specific gene panels (55 index cases). In 61.3% of the patients (n = 214) a genetic diagnosis was established based on pathogenic and likely pathogenic variants. Diagnostic yield was higher in consanguineous families (60.1 vs. 39.5%). In 27 patients, genetic diagnosis relied on additional biochemical testing, allowing rapid assessment of the functional effect of the variants. Remarkably, the genetic diagnosis had a direct impact on clinical management. Most relevant consequences were therapy related such as initiation of the appropriated treatment in a timely manner in 51.9% of the patients (n = 111). Finally, we report 12 candidate genes among 66 cases with no genetic diagnosis. Importantly, three of these genes were validated as 'diagnostic' genes given the strong evidence supporting causality derived from our data repository (CAP2-dilated cardiomyopathy, ITFG2-intellectual disability and USP53-liver cholestasis). The high diagnostic yield, clinical impact, and research findings demonstrate the utility of genomic testing, especially when used as first-line genetic test. For patients with suspected genetic diseases from resource-limited regions, ES can be considered as the test of choice to achieve genetic diagnosis.

Keywords: Genetics research; Medical genetics; Molecular medicine.

Fig. 1. High diagnostic yield and clinical utility.

a High diagnostic yield obtained in 349 index patients. In 214 patients (61.3%) a genetic diagnosis was established based on pathogenic/likely pathogenic variants. b High clinical impact of genetic testing with 170 patients (79.4%) reported with a change in clinical management after establishment of the genetic diagnosis. Venn diagram representing the main categories evaluated and the number of index cases per category/combination.

Fig. 2. Two distinct genetic diseases in one family.

Left: Upper body photograph of male index patient at age of 10 years, with mild dysmorphic features: narrow forehead, thick eyebrows, long eyelashes, mildly upslanted eyes, short palpebral fissure, broad nasal bridge, low hanging columella, short philtrum, thin upper lip and wide mouth, dental malalignment with delayed eruption. A homozygous pathogenic deletion of exon 9 in the L2HGDH gene was detected in this patient by ES. IGV image showing the corresponding region of L2HGDH, with the absence of reads in index patient (area corresponding to exon 9 in red box). Parents and siblings have reduced number of reads consistent with a heterozygous deletion (exon 8 and 10: 100–195 reads, exon 9: 23–35 reads). The findings were confirmed by qPCR. Right: Photograph of female sibling at age of 5 years. A homozygous likely pathogenic variant in the DYM gene was detected in the affected sibling (variant quality score (QS) = 1072, reference value >215). Carrier status of both parents was confirmed. The variant was validated by Sanger sequencing. Parents of the patients provided written informed consent for the use of patient images for scientific publication.

Fig. 3. ITFG2 is a newly identified gene related to neurodevelopmental delay and ataxia.

Index and sister are homozygous for NM_018463.3:c.361C>T, p.Gln121* and parents are confirmed heterozygous carriers. Photographs of male index (12 years old) and female sibling (10 years old) showing mild dysmorphic features. Male index: thick hair, narrow forehead, bushy eyebrows with synophris, almond-shape eyes, long eyelashes, broad nasal bridge, short columella, short and marked philtrum with Cupid bow and small mouth. Sister: narrow forehead, bushy eyebrows with synophris, small eyes almond shaped, short palpebral fissure, long eyelashes, broad and tall nasal bridge, thin lips with small mouth. Corresponding IGV image in exon 4 of ITFG2 is shown (variant QS = 5165 and 4733 in index and sibling, respectively). Parents of the patients provided written informed consent for the use of their children images in scientific publication.