The iHope program enabled cGS testing across a network of 24 clinical sites in the United States, Mexico, Peru, the Democratic Republic of Congo, Ghana, Italy, New Zealand and the United Arab Emirates. Participation was limited to individuals with signs or symptoms indicative of a RGD, consistent with current professional guidelines and prior large RGD population investigations, and limited access to molecular testing.7,9,14,15
Cohort characteristics
A total of 1,004 individuals from 981 families received cGS testing through the iHope program from June 2016 through September 2021 (Fig. 1 and Supplementary Table 1), thirty-four percent (345/1004) of which were from LMIC sites including Mexico (209), Peru (89), the Democratic Republic of Congo (35), Ghana (9) and individual cases from Romania (1), Brazil (1) and India (1) (Fig. 1). Patients were from diverse ancestral backgrounds, with representation from each of seven superpopulations derived from the 1000 Genomes Project, Human Genome Diversity Project and Simons Genome Diversity Project cohorts (Fig. 2A and Supplementary Figs. 1 and 2). A non-European superpopulation was the highest ancestral contributor in 51.8% (521) of the cohort. The distribution of patient age was similar between LMIC and HIC (median age (y) LMIC 6.6 vs HIC 6.3, 95% CI -0.7-1.9, p = 0.36). For sex, the odds ratio male was 1.1 (95% CI 0.8–1.4, p = 0.69) (Fig. 2B). Trio or higher-order family structures including both biological parents were available for the majority of cases (713/1004 [71.0%]).
Patient phenotypes were complex with nervous system, skeletal system, and head or neck the most frequently identified Human Phenotype Ontology root ancestor terms in both LMIC and HIC groups (Fig. 2C). Digestive system (LMIC 24% vs HIC 41%), respiratory system (LMIC 7% vs HIC 24%), and cardiovascular system (LMIC 19% vs HIC 34%) root ancestor terms had the largest proportional difference between LMIC and HIC groups. Patients from HIC sites had an average of 2.3 more phenotypic terms submitted per case (95% CI 1.5–3.1, p < 0.001) but computed phenotypic information content showed no association with likelihood of a positive test result (point estimate 6.4, 95% CI 1.7–11.6, p = 0.17) (Supplementary Fig. 3).
Diagnostic Yield
The total diagnostic yield across the cohort was 41.4% (416/1004), with patients from LMIC sites 2.6-times more likely to receive a positive test result compared to patients from HIC sites (LMIC 195/345 [56.5%] vs HIC 221/659 [33.5%], 95% CI 1.9–3.4, p < 0.0001) (Fig. 3A). In an additional 26.1% of patients inconclusive test results were reported, with a higher proportion reported in patients from HIC sites (195/659, 29.5%) compared to LMIC sites (67/354, 19.4%) (Fig. 3A). Although patients from HIC sites were 6.6-times more likely than patients from LMIC sites to have had a least one prior genetic test (95% CI 4.9–8.8, p < .0001), there was no observed difference in the likelihood of a positive test result based on prior genetic testing within either the HIC or LMIC cohorts (Supplementary Fig. 4).
Reported variants (1,033) spanned the mutational spectrum, including nuclear genome SNVs (714), small indels (130), CNVs (165), STRs (10), mitochondrial SNVs (9), uniparental disomy (3), and spinal muscular atrophy detected by biallelic absence of the c.840C allele (2) (Methods and Supplementary Fig. 5). LMIC patients had a greater proportion of copy number variants reported (LMIC 84/377 [22.3%] vs HIC 81/650 [12.5%]), which spanned a larger size range, compared to HIC patients (Supplementary Figs. 5 and 6).
Diagnostic Evaluation and Change of Management
A cGS impact survey was provided to the ordering clinicians for patients who pursued cGS from June 2016 through October 2020 (Fig. 1 and Supplementary Table 2). Clinical GS impact surveys were completed by a clinical provider for 694 cases (694/1004 [69.1%] of the total cohort) (Fig. 1). Survey response rates were comparable between LMIC and HIC sites (LMIC 254/297 [85.5%] vs HIC 440/521 [84.5%]) and were highest for patients with positive test results (LMIC 157/172 [91.3%] vs HIC 162/176 [92.0%]) compared to inconclusive (LMIC 44/57 [77.2%] vs HIC 122/148 [82.4%]) or negative test results (LMIC 53/68 [77.9%] vs HIC 156/197 [79.2.0%]).
To control for the elevated LMIC diagnostic yield, and the potential influence of LMIC or HIC site designation on DE and COM, which is mediated by test result category (Supplementary Fig. 7), comparative analyses of GS test impact were stratified by test result category. Clinical GS results impacted DE in 514 of 668 patients (76.9%) and was more common in patients from LMIC sites regardless of test result category (LMIC 221/253 [87.4%] vs HIC 293/415 [70.1%], OR 2.2, 95% CI 1.3–3.6, p < 0.0001) (Fig. 3C and Supplementary Table 3). Across both cohorts, patients with a positive test result were 64.2-times more likely to have an impact to DE (95% CI 32.5-202.8, p < 0.0001) (Fig. 3C). Clinical GS findings led to a change in the clinical diagnosis in 326 of 694 patients (46.9%). Positive test results corresponded to the highest rates of change in clinical diagnosis and were comparable between HIC and LMIC sites (HIC 130/163 [79.8%] vs LMIC 122/157 [77.7%], OR 0.9, CI 95% 0.5–1.5, p = 0.50) (Fig. 3B).
Overall, clinical GS resulted in COM in 285 of 694 patients (41.1%), inclusive of specialty referrals, imaging and testing, therapeutic interventions and palliative care (Fig. 4). When comparing across GNI site designations, patients with a positive test result from LMIC sites were equally likely to experience a COM compared to patients with a positive test result from HIC sites (OR 0.9, 95% CI 0.5–1.4, p = 0.49), and no statistically significant differences were observed for inconclusive or negative test results (Supplementary Table 3). When genetic counseling and avoidance of additional testing were also considered, a total of 480 patients (69.2%) experienced COM (LMIC 198/254 [77.9%] vs HIC 282/440 [64.1%]) (Fig. 4). Overall, genetic counseling was the most frequently endorsed change in management category (377/602 [62.6%]), followed by referrals, imaging and testing (265/617 [42.9%]), avoidance of additional testing (198/668 [29.6%]), therapeutics (72/575 [12.3%]) and palliative care (23/694 [3.3%]) (Fig. 4, Supplementary Fig. 8). Therapeutic COM was endorsed in 72 patients and was comparable between HIC and LMIC sites (HIC 42/353 [11.9%] vs LMIC 30/222 [13.5%], OR 0.9, 95% CI 0.5–1.5, p = 0.62) (Fig. 4A and C).
Amongst LMIC cases, six notable cGS diagnoses with changes of management were described (Table 1). For example, in a 22-year-old Peruvian female with early-onset spastic paraparesis and lower limb hyperreflexia, and classic spastic gait, cGS identified a heterozygous, paternally inherited inframe insertion in the GCH1 gene, classified as likely pathogenic for autosomal dominant GTP cyclohydrolase-1-deficiency (OMIM # 128230). This finding resulted in a change of the patient’s clinical diagnosis from early-onset hereditary spastic paraparesis to dopa responsive dystonia (DRD), and both she and her affected father, previously diagnosed with sporadic early-onset parkinsonism, responded to low doses of levodopa with almost complete control of symptoms.
Table 1
Notable LMIC Patient Management Changes. yo: years old; m: male sex; f: female sex; (G.XX.X): ICD code provided by clinician; kb: kilobase; PO: proband-only analysis; AD: autosomal dominant inheritance of the preceding disorder; XL: X-Linked inheritance of preceding disorder; LP- likely pathogenic variant classification; P- pathogenic variant classification; ID: intellectual disability; DD: developmental delay; NDD: neurodevelopmental delay; Het: heterozygous
Study ID,
Location,
age (sex)
|
Phenotype
|
Clinical Diagnosis Prior to cGS
|
cGS Finding & Disorder
|
Change in Management
|
00638
Peru
9 yo (m)
|
Early-onset generalized dystonia, hyperreflexia, knee pain, cramping, bilateral renal hydronephrosis
|
Early-onset dystonia, (G24.9)
|
Het. 71 kb deletion including exon 1 of GCH1; unknown inheritance (PO); P; Dopa-responsive dystonia (AD)
|
Low doses of levodopa/
decarboxylase inhibitor
|
00800
Peru
22 yo (f)
|
Early onset spastic paraparesis with lower limb hyperreflexia, spastic gait, mild scoliosis, pes equinovarus
|
Early-onset spastic paraplegia (G11.4)
|
Het. paternally inherited in-frame insertion in GCH1; LP; GTP
cyclohydrolase − 1-deficiency (AD)
|
Low doses of levodopa/decarboxylase inhibitor
|
00316 Mexico
2 yo (f)
|
Muscle hypotonia, hyporeflexia, foot malposition, myopathic facies, normal early motor development but unable to walk independently
|
Spinal muscular atrophy
|
Absence of the SMN1 c.840C allele, which is consistent with an
absence of wild-type SMN1 & predicted to result in spinal muscular atrophy
|
Nusinersen
|
00818
Peru
14 yo (m)
|
Moderate ID, DD, short stature, epilepsy, obesity, aggressive behavior, poor attention & dysmorphic facial features
|
Undiagnosed ID with obesity & short stature
|
Het. de novo missense variant in SLC2A1; P; glucose transporter type I deficiency syndrome (AD)
|
Ketogenic diet with carnitine supplementation
|
00346
Mexico
10 yo (m)
|
Progressive hypotonia, weakness & muscle atrophy especially pronounced in lower extremities & proximal limbs, elevated CK
|
Undiagnosed muscular dystrophy
|
Hemizygous, maternally inherited intronic variant in DMD; LP; Dystrophinopathies (XL)
|
Cardiology referral, deflazacort recommended
|
00338
Mexico
3 yo (m)
|
Epilepsy, heterotopia, NDD, allergic rhinitis, cerebral palsy, generalized weakness, uncoordinated walk, hypertrichosis, minor dysmorphic features, focal cortical dysplasia.
|
Undiagnosed developmental disorder
|
Het. de novo missense variant in GFAP; P; Alexander disease (AD)
|
Recommended to follow neuroprotective measures such as avoiding long fasting periods, flickering lights & continuing care with a neuro-pediatrician.
|