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Case Reports
. 2024 Jan;12(1):e2285.
doi: 10.1002/mgg3.2285. Epub 2023 Sep 23.

Clinical application of targeted long read sequencing in prenatal beta-thalassemia testing and genetic counseling

Hui-Lin Chin  1   2 , Miles C Benton  3 , Lin Yang  3 , Kok Siong Poon  4 , Karen M L Tan  4 , Saumya S Jamuar  5 , Roger Foo  6 , Hai Yang Law  7 , Denise Li-Meng Goh  1   2 , Samuel S Chong  2   4   8 , Paola Florez de Sessions  3
Affiliations
Case Reports

Clinical application of targeted long read sequencing in prenatal beta-thalassemia testing and genetic counseling

Hui-Lin Chin et al. Mol Genet Genomic Med. 2024 Jan.

Abstract

Background: Beta thalassemia, related to HBB mutation and associated with elevated hemoglobin A2 (HbA2), is an important genetic hemoglobinopathy with high incidences of disease and carrier rates in Singapore. Carrier screening is essential to facilitate prenatal counseling and testing. However, when individuals with elevated HbA2 do not have an identifiable HBB disease-associated variant, there is ambiguity on risk to their offspring.

Methods: We describe a case report of a proband with elevated HbA2, no identifiable HBB disease-associated variant, whose partner was a beta thalassemia carrier. Through clinical HBB gene sequencing, multiplex ligation-dependent probe amplification (MLPA) analysis, as well as targeted Nanopore long read sequencing of selected genes, we performed a complete analysis of HBB including the promoter region, 5'UTR and coding gene sequence, as well as evaluation for potential modifier variants and other rare structural variants.

Results: This process identified that the proband was heterozygous for KLF1:c.544T>C (p.Phe182Leu), a potential functional polymorphism previously known to be associated with benign elevated HbA2 levels. The presence of disease variants in the HBB locus was excluded.

Conclusion: This finding provided clarity and enabled family planning for the proband and her family.

Keywords: Beta-thalassemia; Carrier testing; Elevated HbA2; Long read sequencing; Modifier variants.

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Conflict of interest statement

P.F.d.S., L.Y., and M.C.B., are full‐time employees of, and share/phantom shareholders in, Oxford Nanopore Technologies and Oxford Nanopore provided certain flow cells and services in support of the research. Oxford Nanopore Technologies products are intended for molecular biology applications and are not intended for diagnostic purposes.

Figures

FIGURE 1
FIGURE 1
IGV view of the KLF1:c.544T>C (p.Phe182Leu) variant identified in the proband using targeted Nanopore long read sequencing.
See this image and copyright information in PMC

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