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. 2025 Jul 10;6(3):100430.
doi: 10.1016/j.xhgg.2025.100430. Epub 2025 Apr 7.

Multiple molecular diagnoses identified through genome sequencing in individuals with suspected rare disease

Alka Malhotra  1 , Erin Thorpe  2 , Alison J Coffey  3 , Revathi Rajkumar  3 , Josephine Adjeman  4 , Naomi Dianne Naa Adjeley Adjetey  5 , Sharron Aglobitse  4 , Felix Allotey  6 , Todor Arsov  7 , Joyce Ashong  8 , Ebenezer Vincent Badoe  4 , Donald Basel  9 , Yvonne Brew  10 , Chester Brown  11 , Kerri Bosfield  11 , Kari Casas  12 , Mario Cornejo-Olivas  13 , Laura Davis-Keppen  14 , Abbey Freed  15 , Kate Gibson  16 , Parul Jayakar  17 , Marilyn C Jones  18 , Martina Kawome  19 , Aimé Lumaka  20 , Ursula Maier  21 , Prince Makay  20 , Gioconda Manassero  22 , Marilyn Marbell-Wilson  23 , Charles Marcuccilli  24 , Diane Masser-Frye  18 , Julie McCarrier  9 , Hannah-Sharon Mills  4 , Jeny Balazar Montoya  22 , Gerrye Mubungu  20 , Mamy Ngole  20 , Jorge Perez  25 , Eniko Pivnick  11 , Milagros M Duenas-Roque  26 , Hildegard Pena Salguero  27 , Arturo Serize  25 , Marwan Shinawi  28 , Fabio Sirchia  29 , Claudia Soler-Alfonso  30 , Alan Taylor  31 , Lauren Thompson  17 , Gail Vance  32 , Adeline Vanderver  33 , Keith Vaux  34 , Danita Velasco  35 , Samuel Wiafe  36 ; Illumina Laboratory Services Interpretation and Reporting Team  3 ; Ryan J Taft  2 , Denise L Perry  3 , Akanchha Kesari  37
Affiliations

Multiple molecular diagnoses identified through genome sequencing in individuals with suspected rare disease

Alka Malhotra et al. HGG Adv. .

Abstract

Genome sequencing is a powerful and comprehensive test that detects multiple variants of different types. The interrogation of variants across the genome enables the identification of multiple molecular diagnoses (MMDs) in a single individual. In this retrospective study, we describe individuals in whom MMDs were associated with the proband's indication for testing (IFT), secondary findings, or incidental findings. An MMD is considered where at least one of the findings is associated with the primary IFT and all variants are classified as either likely pathogenic or pathogenic. Clinical genome sequencing was performed for all individuals as part of the iHope program at the Illumina Laboratory Services between September 2017 and December 2023. The iHope cohort included 1,846 affected individuals, with 872 (47.2%) found to have at least one likely pathogenic or pathogenic variant associated with the primary IFT. Of these, 81 (9.3%) individuals had multiple clinically significant molecular findings, including 76 individuals with reported variants associated with 2 different conditions, and 5 individuals with more than 2 molecular findings. A total of 32 individuals (3.7%) had at least 2 molecular diagnoses related to the primary IFT, while in 49 (5.6%) individuals, the variant(s) reported for the second condition constituted a secondary or incidental finding. Our study highlights that among individuals with a likely pathogenic or pathogenic finding identified through genome sequencing, 9% have MMDs, which may have been missed with different testing methods. Of note, approximately 60% of the 81 individuals with an MMD had a potentially actionable secondary or incidental finding.

Keywords: WGS; incidental finding; multiple molecular diagnoses; rare disease; secondary finding.

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Conflict of interest statement

Declaration of interests A.J.C., A.K., A.M., D.L.P., E.T., R.J.T., R.R., and the Illumina Laboratory Services Interpretation and Reporting Team are either current or former employees and shareholders at Illumina, Inc.

Figures

Figure 1
Figure 1
Breakdown of report outcome for all cases (N = 1,846) Negative report issued = 974; positive report issued with single finding = 791; positive with multiple findings = 81, including 32 with multiple primary findings, 19 with primary and secondary findings, and 30 with primary and incidental findings.
Figure 2
Figure 2
Number of molecular diagnoses identified per individual among the 81 individuals
Figure 3
Figure 3
Variant types and overall percentage detected in individuals with multiple molecular findings CNV, copy-number variant; MT, mitochondrial variant; SNV, single-nucleotide variant; STR, short tandem repeat; SV, structural variant.
See this image and copyright information in PMC

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