Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) for the Diagnosis of Thalassemia

Hassan, Syahzuwan; Bahar, Rosnah; Johan, Muhammad Farid; Hashim, Ezzeddin Kamil Mohamed Mohamed; Abdullah, Wan Zaidah; Esa, Ezalia; Hamid, Faidatul Syazlin Abdul; Zulkafli, Zefarina

doi:10.3390/diagnostics13030373

Cited by 20 publications

(16 citation statements)

References 135 publications

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“…According to the present study different abnormalities were found in the evaluated patients and it was observed that eye abnormalities were found with high frequency of 35% followed by skin abnormality 17%, bone and joint abnormality13 %, ear abnormality 8% and mental abnormality 02 % while 25 % of evaluated member of the population were normal with no visible physical abnormality. The present study has some similarities with the study performed by Erickson et al, (1980) 27 . According to their study 15% of patients were having Superficial skin infections (tinea versicolor, other scabies, mycosis and pediculosis), 10% with psychiatric problems, 8% were having Otorhinological problems (deafness, otitis media, chronic sinusitis), and 6% were having opthalmological problems (conjunctivitis, cataract) 28 .…”

Section: Discussionsupporting

confidence: 91%

Prevalence and Clinical Features of Thalassemia Minor Cases

Faizan¹,

Rashid²,

Hussain³

et al. 2023

PJMHS

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Background: Thalassemia, the most common heterogeneous single gene disorder causing sever genetic health problem in the world. In 1932 George and William gave it the name thalassemia derived from Greek words (“thallassa: mean sea) and (“aima: mean blood). The research was conducted on thalassemia minor patients in North Waziristan and some selected areas of Peshawar Khyber pakhtunkhwa. Methods: During this survey 100 thalassemia minor patients were interviewed belonging to different castes. It was observed that majority of the patients were from the age group 1-10 years both in male asn females. Different ethnic groups were interviewed such as Yousafzai, Halimzai, Dawar, Wazir, Noor khel, Musazai, Saidan, Miserkhal, Afridi, Miagan, and Afghan. Results: The most of the thalassemia minor patients belonged to rural area (62.4 %) while 36.6% patients were reported from urban area. The maximum number of thalassemia minor patients belonged to lower class which was reported 47% followed by middle class (35%) and rich people (18%). The parents of 64 patients were cousin while the parents of 36 patients had marriage out of the family. The birth abnormalities were also recorded and observed as abortion (30%), delay birth (23%), still birth (13%) and premature birth (17%). During this study it was observed that majority of the patients were of the moderate body status (54.5%) Interestingly the ratio of obese people was very low. While the ratio of thin people was 39.4%. The physical abnormalities found in thalassemia minor patients included eye, skin, ear, mental and bone and joint abnormalities. the people having the age from 1-10 have an average HB level of 9.45 g/dl while those having age of 41-60 have an average HB level of 11.58 g/dl. The physical infections also reported such as eye infection (39%), GIT infection (20%), Lung infection, Skin infection (16%), UTI (7%) and Ear infection (2%). Conclusion: This study provides an insight in to the mechanism of transmission of thalassemia in the family and suggest social awareness about the disadvantages of the interfamilial marriages. Keywords: Thalassemia, Consanguineous marriages, Hemoglobin, Birth Abnormalities, Infections.

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Section: Discussionsupporting

confidence: 91%

Prevalence and Clinical Features of Thalassemia Minor Cases

Faizan¹,

Rashid²,

Hussain³

et al. 2023

PJMHS

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“…Compared with the second-generation sequencing technology, TGS technology overcomes some NGS shortcomings in genome assembly. TGS does not require polymerase chain reaction (PCR) amplification or long read length and has no guanine-cytosine (GC) preference, thus making genome assembly using PacBio Hi-Fi an effective assembly strategy [ 29 , 30 ]. Compared with the previously published 841 Mb (N50 = 122 kb) genome assembly of white clover, the genome size in this study was 1,095 Mb (contig N50 = 14 Mbp), indicating a significantly improved quality.…”

Section: Discussionmentioning

confidence: 99%

High-quality chromosome-level de novo assembly of the Trifolium repens

Wang

et al. 2023

BMC Genomics

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Background White clover (Trifolium repens L.), an excellent perennial legume forage, is an allotetraploid native to southeastern Europe and southern Asia. It has high nutritional, ecological, genetic breeding, and medicinal values and exhibits excellent resistance to cold, drought, trample, and weed infestation. Thus, white clover is widely planted in Europe, America, and China; however, the lack of reference genome limits its breeding and cultivation. This study generated a white clover de novo genome assembly at the chromosomal level and annotated its components. Results The PacBio third-generation Hi-Fi assembly and sequencing methods generated a 1096 Mb genome size of T. repens, with contigs of N50 = 14 Mb, scaffolds of N50 = 65 Mb, and BUSCO value of 98.5%. The newly assembled genome has better continuity and integrity than the previously reported white clover reference genome; thus provides important resources for the molecular breeding and evolution of white clover and other forage. Additionally, we annotated 90,128 high-confidence gene models from the genome. White clover was closely related to Trifolium pratense and Trifolium medium but distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum. The expansion, contraction, and GO functional enrichment analysis of the gene families showed that T. repens gene families were associated with biological processes, molecular function, cellular components, and environmental resistance, which explained its excellent agronomic traits. Conclusions This study reports a high-quality de novo assembly of white clover genome obtained at the chromosomal level using PacBio Hi-Fi sequencing, a third-generation sequencing. The generated high-quality genome assembly of white clover provides a key basis for accelerating the research and molecular breeding of this important forage crop. The genome is also valuable for future studies on legume forage biology, evolution, and genome-wide mapping of quantitative trait loci associated with the relevant agronomic traits.

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“…Large deletions are typically found by gap-PCR or MLPA, while point mutations and indels are typically detected by MARMS-PCR or sequencing. A homozygous β-thalassemia detected using MARMS-PCR and sequencing may not be a true homozygote but rather a compound heterozygote with a deletional β-thalassemia or a δβ-thalassemia that must be ruled out using gap-PCR, MLPA, or cascade screening [ 26 ]. Therefore, a few countries have recently introduced screening for thalassemia or hemoglobinopathies using next-generation sequencing (NGS).…”

Section: Discussionmentioning

confidence: 99%

Application of Targeted Next-Generation Sequencing for the Investigation of Thalassemia in a Developing Country: A Single Center Experience

et al. 2023

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Thalassemia is identified as a prevalent disease in Malaysia, known to be one of the developing countries. Fourteen patients with confirmed cases of thalassemia were recruited from the Hematology Laboratory. The molecular genotypes of these patients were tested using the multiplex-ARMS and GAP-PCR methods. The samples were repeatedly investigated using the Devyser Thalassemia kit (Devyser, Sweden), a targeted NGS panel targeting the coding regions of hemoglobin genes, namely the HBA1, HBA2, and HBB genes, which were used in this study. There were many different genetic variants found in 14 unrelated cases. Out of all fourteen cases, NGS was able to determine an additional -50 G>A (HBB:c.-100G>A) that were not identified by the multiplex-ARMS method, including HBA2 mutations, namely CD 79 (HBA2:c.239C>G). Other than that, CD 142 (HBA2:c.427T>C) and another non-deletional alpha thalassemia and alpha triplication were also not picked up by the GAP-PCR methods. We illustrated a broad, targeted NGS-based test that proposes benefits rather than using traditional screening or basic molecular methods. The results of this study should be heeded, as this is the first report on the practicality of targeted NGS concerning the biological and phenotypic features of thalassemia, especially in a developing population. Discovering rare pathogenic thalassemia variants and additional secondary modifiers may facilitate precise diagnosis and better disease prevention.

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Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) for the Diagnosis of Thalassemia

Cited by 20 publications

References 135 publications

Prevalence and Clinical Features of Thalassemia Minor Cases

Prevalence and Clinical Features of Thalassemia Minor Cases

High-quality chromosome-level de novo assembly of the Trifolium repens

Application of Targeted Next-Generation Sequencing for the Investigation of Thalassemia in a Developing Country: A Single Center Experience

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