Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Case Reports
. 2024 Mar 1;109(3):1000-1006.
doi: 10.3324/haematol.2023.282902.

An unusual case of thalassemia intermedia with inheritable complex repeats detected by single-molecule optical mapping

Qianqian Zhang  1 , Peng Lin  1 , Aiping Mao  2 , Yongqiong Liu  3 , Xuan Shang  3 , Xiaofeng Wei  3 , Yuezhen Li  2 , Bin Lin  4 , Xiangmin Xu  5
Affiliations
Case Reports

An unusual case of thalassemia intermedia with inheritable complex repeats detected by single-molecule optical mapping

Qianqian Zhang et al. Haematologica. .
No abstract available

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Hematological and molecular data of the pedigree. (A) Longitudinal hematological features of the proband. The highest and lowest values are labeled on the figure. (B) Pedigree of the investigated family with copy number variations of the α-globin cluster. The proband is indicated by the arrow. (C) The Southeast Asian type deletion (--SEA, SEA deletion) detected in the proband (III-1) and mother (II-2) by agarose gel electrophoresis and gap-polymerase chain reaction (gap-PCR). (D) The multiplex ligation dependent probe amplification (MLPA) results targeting α-globin cluster among the family members. The histogram shows duplication of the 4.2-kb fragment for I-2, II-1, and III-1. II-2 and III-1 both carried the SEA deletion. The targeting regions of each specific probe are indicated below. (E) Targeting regions of the droplet digital PCR (ddPCR) probes. (F) The copy number values of the 4 family members as determined by ddPCR. Normal controls, -α3.7/αα and -α4.2/αα samples were tested using 2 biological and 2 analytical repeats. Samples from 4 family members were tested using 2 analytical repeats. (G) Representative reads from long-read sequencing of II-1. The allele with anti-4.2 repeats (read 1/2/3) and wild-type allele (read 4). Raw reads were aligned to hg38, cut at positions chr16:169454 and chr16:173711, and then displayed in integrative genomics viewer plot from left to right and from top to bottom. (H) The ratios of α- to β-globin chains were calculated by reversed-phase high performance liquid chromatograph (LC-20AT, Shimadzu Corporation, Kyoto, Japan). Normal controls, SEA deletion carriers and HbH diseases samples were tested using 2 biological and 2 analytical repeats. Samples from II-1, II-2, and III-1 were tested using 2 analytical repeats. There were no significant differences in α/β ratios among the 4 groups (normal controls, II-1, II-2, and SEA deletion carriers). The α/β ratios of III-1 were significantly lower than those of II-1, II-2 and the SEA deletion carriers, but higher than the HbH diseases samples. (I) Real-time quantitative PCR (RT-qPCR) for assessing the α-globin mRNA level. α-globin mRNA was slightly decreased in II-1 with no significance, decreased by 50% in II-2, while more decreased in III-1.
Figure 2.
Figure 2.
Characterization of the duplications by single-molecule optical mapping technology. Single-molecule optical mapping analysis of the proband (A), I-2 (B) and II-1 (C). Schematic representation showing the locations of α-globin genes and the region of 3 copy number variations (-α3.7, -α4.2, --SEA) are present above the each panel. The α-globin cluster reference maps (green) aligned to the 2 alleles maps (blue) are indicted by horizontal boxes. The vertical lines within boxes are label sites. Matching labels between alleles from samples and reference genome maps are connected by gray lines. In Allele-1, the distance between the 2 labels, 222,575 and 226,379, was much larger than that of the reference genome, indicating sequence insertion. The pattern of label 220,259 to label 222,575 was amplified with extra 24 regular repeats compared to reference genome. The 24 extra tandem duplications of the 4.2-kb segment in Allele-1 are indicated by red dotted lines. In Allele-2 of the proband (A), the distance between the 2 labels, 211,806 and 234,893, was shorter than that of the reference genome, indicating sequence deletion. The SEA deletion region in Allele-2 is indicated by a purple line. Coordinates are based on human genome build GRCh37/hg19.
Figure 3.
Figure 3.
A hypothetical model to explain that the tandemly repeated copies of HBA2 inhibit the normal α-globin expression. (A) The α-globin locus in human, including HBZ, HBA2, HBA1 and 4 multispecies conserved sequences (MCS R1-4)) associated with erythroid-specific DNase1 hypersensitive sites (HS) (upper panel). Normally, HS contact α-globin gene promoters via chromatin looping, facilitated by the erythroid-specific transcription factors and proteins, activates high-level transcription of the cis-linked α-globin genes (bottom panel). (B) The inheritable complex repeats detected in this study, inserted 24 extra α-globin genes between HBA2 and HBA1 (upper panel). The repeats largely extend the distance between the HS and HBA1 by approximately 100 kb, diminish HS/HBA1 contacts, thus the HBA1 expression is impaired.
See this image and copyright information in PMC

References

    1. Vijian D, Wan Ab Rahman WS, et al. . Molecular detection of alpha thalassemia: a review of prevalent techniques. Medeni Med J. 2021;36(3):257-269. - PMC - PubMed
    1. Chiba K, Shiraishi Y, Nagata Y, et al. . Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data. Bioinformatics. 2015;31(1):116-118. - PubMed
    1. Shang X, Xu XM. Update in the genetics of thalassemia: what clinicians need to know. Best Pract Res Clin Obstet Gynaecol. 2017;39:3-15. - PubMed
    1. Shang X, Peng ZY, Ye YH, et al. . Rapid targeted next-generation sequencing platform for molecular screening and clinical genotyping in subjects with hemoglobinopathies. EBioMedicine. 2017;23:150-159. - PMC - PubMed
    1. Mantere T, Neveling K, Pebrel-Richard C, et al. . Optical genome mapping enables constitutional chromosomal aberration detection. Am J Hum Genet. 2021;108(8):1409-1422. - PMC - PubMed

Publication types