Evidence of recent natural selection on the Southeast Asian deletion (--(SEA)) causing α-thalassemia in South China

Molecular patterns of alpha-thalassemia in the kingdom of Saudi Arabia: identification of prevalent genotypes and regions with high incidence

BACKGROUND

Alpha-thalassemia (α-thalassemia) is one of the most common monogenic diseases in Saudi Arabia and is associated with significant morbidity. Premarital testing programs in Saudi Arabia reduce the burden of hemoglobinopathy disorders, and ongoing monitoring is required. We aimed to explore the molecular nature of α-globin genes and identify the most common genotypes and regions with a high risk of α-thalassemia in Saudi Arabia.

METHODS

This retrospective study was conducted between January 2021 and December 2022. Six hundred twenty-five samples from patients with microcytic hypochromic anemia in Saudi Arabia were analyzed using reverse dot blot hybridization (RDBH)-based multiplex-PCR, which screens for the known 21 mutations of α-globin genes.

RESULTS

Seven mutations in the α-globin gene were identified in 88.96% (556) patients. The most frequent abnormality of a-globin genes was -α3.7 (62.3%), followed by α2IVS1(-5nt) (20.7%) and α2 polyA-1 (α2T.Saudi) (14.1%). Interestingly, α2 polyA-2 (α2T.Turkish) was identified in Saudi and presented with -MED, causing Haemoglobin H disease. The incidence of α-thalassemia in Saudi Arabia's cities showed significant differences (P = 0.004). Jeddah City had the highest percentage of cases (25%), followed by Makkah (23%), Taif (13.3%), and Al-Ahassa (12.4%).

CONCLUSION

The study provides current knowledge about the molecular nature of α- thalassemia, highlights the common genotypes that could contribute to disease occurrence in the Saudi population, and sheds light on Saudi regions with a high incidence. It also recommends further studies in a larger population and with differently composed molecular assays to verify these findings.

A pangenome reference of 36 Chinese populations

Human genomics is witnessing an ongoing paradigm shift from a single reference sequence to a pangenome form, but populations of Asian ancestry are underrepresented. Here we present data from the first phase of the Chinese Pangenome Consortium, including a collection of 116 high-quality and haplotype-phased de novo assemblies based on 58 core samples representing 36 minority Chinese ethnic groups. With an average 30.65× high-fidelity long-read sequence coverage, an average contiguity N50 of more than 35.63 megabases and an average total size of 3.01 gigabases, the CPC core assemblies add 189 million base pairs of euchromatic polymorphic sequences and 1,367 protein-coding gene duplications to GRCh38. We identified 15.9 million small variants and 78,072 structural variants, of which 5.9 million small variants and 34,223 structural variants were not reported in a recently released pangenome reference¹. The Chinese Pangenome Consortium data demonstrate a remarkable increase in the discovery of novel and missing sequences when individuals are included from underrepresented minority ethnic groups. The missing reference sequences were enriched with archaic-derived alleles and genes that confer essential functions related to keratinization, response to ultraviolet radiation, DNA repair, immunological responses and lifespan, implying great potential for shedding new light on human evolution and recovering missing heritability in complex disease mapping.

Balancing selection on genomic deletion polymorphisms in humans

A key question in biology is why genomic variation persists in a population for extended periods. Recent studies have identified examples of genomic deletions that have remained polymorphic in the human lineage for hundreds of millennia, ostensibly owing to balancing selection. Nevertheless, genome-wide investigation of ancient and possibly adaptive deletions remains an imperative exercise. Here, we demonstrate an excess of polymorphisms in present-day humans that predate the modern human-Neanderthal split (ancient polymorphisms), which cannot be explained solely by selectively neutral scenarios. We analyze the adaptive mechanisms that underlie this excess in deletion polymorphisms. Using a previously published measure of balancing selection, we show that this excess of ancient deletions is largely owing to balancing selection. Based on the absence of signatures of overdominance, we conclude that it is a rare mode of balancing selection among ancient deletions. Instead, more complex scenarios involving spatially and temporally variable selective pressures are likely more common mechanisms. Our results suggest that balancing selection resulted in ancient deletions harboring disproportionately more exonic variants with GWAS (genome-wide association studies) associations. We further found that ancient deletions are significantly enriched for traits related to metabolism and immunity. As a by-product of our analysis, we show that deletions are, on average, more deleterious than single nucleotide variants. We can now argue that not only is a vast majority of common variants shared among human populations, but a considerable portion of biologically relevant variants has been segregating among our ancestors for hundreds of thousands, if not millions, of years.

Epidemiology, evolutionary origin, and malaria-induced positive selection effects of G6PD-deficient alleles in Chinese populations

BACKGROUND

Although glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common inherited disorder in the Chinese population, there is scarce evidence regarding the epidemiology, evolutionary origin, and malaria-induced positive selection effects of G6PD-deficient alleles in various Chinese ethnic populations.

METHODS

We performed a large population-based screening (n = 15,690) to examine the impact of selection on human nucleotide diversity and to infer the evolutionary history of the most common deficiency alleles in Chinese populations.

RESULTS

The frequencies of G6PD deficiency ranged from 0% to 11.6% in 12 Chinese ethnic populations. A frequency map based on geographic information showed that G6PD deficiency was highly correlated with historical malaria prevalence in China and was affected by altitude and latitude. The five most frequently occurring G6PD gene variants were NM_001042351.3:c.1376G>T, NM_001042351.3:c.1388G>A, NM_001042351.3:c.95A>G, NM_001042351.3:c.1311T>C, and NM_001042351.3:c.1024C>T, which were distributed with ethnic features. A pathogenic but rarely reported variant site (NM_001042351.3:c.448G>A) was identified in this study. Bioinformatic analysis revealed a strong and recent positive selection targeting the NM_001042351.3:c.1376G>T allele that originated in the past 3125 to 3750 years and another selection targeting the NM_001042351.3:c.1388G>A allele that originated in the past 5000 to 6000 years. Additionally, both alleles originated from a single ancestor.

CONCLUSION

These results indicate that malaria has had a major impact on the Chinese genome since the introduction of rice agriculture.

Umbilical Cord Blood Screening for the Detection of Common Deletional Mutations of α-Thalassemia in Bangladesh

α-Thalassemia (α-thal) is assumed to be very prevalent in Bangladesh. We aimed to assess the prevalence of the disease in the country and provide a model for α-thal newborn screening in Bangladesh. We collected umbilical cord blood (UCB) samples from 413 unrelated newborns in Bangladesh. Demographic information, blood indices, osmotic fragility, serum iron (Fe), and zinc (Zn) levels were evaluated for all the subjects. All subjects underwent a polymerase chain reaction (PCR)-based diagnosis for α-thal status, followed by a multiplex gap-PCR-based identification of the deletion type present. Sixty-seven subjects had at least one α-thal deletion (16.22%). We observed that -α^3.7 (rightward), - -^SEA (Southeast Asian), -α^4.2 (leftward), - -^MED (Mediterranean) and - -^THAI (Thailand) deletions were the most common α-globin deletions present in the country, with the -α^3.7 (n = 37) and - -^SEA (n = 18) being most prevalent. The osmotic fragility test (OFT) could predict the presence of α-thal deletions with over 98.0% sensitivity. Complete UCB count analysis revealed significant differences between healthy subjects and subjects with α-thal deletions. Although the iron level was almost the same (108.0 vs. 105.7 µg/dL), a reduced level of Zn (98.6 vs. 71.8 µg/dL, p < 0.01) was observed in the cord blood-derived serum of the subjects with α-thal deletions. Moreover, parental age at the time of delivery, gestational period, and birth weight was lower in the subjects with α-thal deletions. This study provides partial information on the epidemiology of α-thal in Bangladesh and describes a model for α-thal newborn screening in the country.

Copy number variation in human genomes from three major ethno-linguistic groups in Africa

Background

Copy number variation is an important class of genomic variation that has been reported in 75% of the human genome. However, it is underreported in African populations. Copy number variants (CNVs) could have important impacts on disease susceptibility and environmental adaptation. To describe CNVs and their possible impacts in Africans, we sequenced genomes of 232 individuals from three major African ethno-linguistic groups: (1) Niger Congo A from Guinea and Côte d’Ivoire, (2) Niger Congo B from Uganda and the Democratic Republic of Congo and (3) Nilo-Saharans from Uganda. We used GenomeSTRiP and cn.MOPS to identify copy number variant regions (CNVRs).

Results

We detected 7608 CNVRs, of which 2172 were only deletions, 2384 were only insertions and 3052 had both. We detected 224 previously un-described CNVRs. The majority of novel CNVRs were present at low frequency and were not shared between populations. We tested for evidence of selection associated with CNVs and also for population structure. Signatures of selection identified previously, using SNPs from the same populations, were overrepresented in CNVRs. When CNVs were tagged with SNP haplotypes to identify SNPs that could predict the presence of CNVs, we identified haplotypes tagging 3096 CNVRs, 372 CNVRs had SNPs with evidence of selection (iHS > 3) and 222 CNVRs had both. This was more than expected (p < 0.0001) and included loci where CNVs have previously been associated with HIV, Rhesus D and preeclampsia. When integrated with 1000 Genomes CNV data, we replicated their observation of population stratification by continent but no clustering by populations within Africa, despite inclusion of Nilo-Saharans and Niger-Congo populations within our dataset.

Conclusions

Novel CNVRs in the current study increase representation of African diversity in the database of genomic variants. Over-representation of CNVRs in SNP signatures of selection and an excess of SNPs that both tag CNVs and are subject to selection show that CNVs may be the actual targets of selection at some loci. However, unlike SNPs, CNVs alone do not resolve African ethno-linguistic groups. Tag haplotypes for CNVs identified may be useful in predicting African CNVs in future studies where only SNP data is available.

Strong Linkage of the Single Nucleotide Polymorphism rs77308790 with an α0-Thalassemia (- -SEA deletion) Allele and Application for Double-Check Diagnosis of Hb Bart's Hydrops Fetalis Syndrome in Thailand

The α⁰-thalassemia (α⁰-thal) [- -^SEA (Southeast Asian) deletion] is highly prevalent in Southeast Asia and South China. The linkage between the single nucleotide polymorphism (SNP) rs77308790 and the - -^SEA deletion was reported in the Chinese population. This study reported the genotype of SNP rs77308790 using the high resolution melting (HRM) curve analysis in the Thai population and the application for double-checking diagnosis of Hb Bart's (γ4) hydrops fetalis syndrome. A total of 202 samples, including α⁰-thal carriers (- -^SEA/αα) (n = 99) and wild-type (n = 103), was recruited. Minor allele frequency (MAF) of SNP rs77308790 (T allele) represented a significant difference (p<0.001) between carrier (- -^SEA deletion) (MAF 0.455) and wild-type (MAF 0.039). The T allele of SNP rs77308790 showed a strong linkage with the - -^SEA deletion allele [correlation coefficient between pairs of loci (D' = 1)] based on constructed random samples (CRSs) in Thais. Moreover, worldwide populations, based on the 1000Genomes database, also found the T allele to be less than 1.0%. For providing a double-checked diagnosis, two SNP (rs3760053, rs77308790) genotypes showed 100.0% concordance with a conventional gap-polymerase chain reaction (gap-PCR) method in nine families at-risk for Hb Bart's hydrops fetalis. The double-checked diagnosis based on the two SNPs (rs3760053, rs77308790) is suitable for implementation in routine diagnosis of Hb Bart's hydrops fetalis syndrome. Furthermore, our HRM analysis system can be amplified with a small amount of fetal DNA and could avoid allele dropouts.

Regional gender differences in an autosomal disease result in corresponding diversity differences

Regional gender differences in autosomal chromosome disorders have been observed repeatedly. However, the corresponding diversity changes remain unconfirmed. By analyzing previously published thalassemia data from the Dai people in Dehong and Xishuangbanna (two regions in Yunnan Province, China), we found that several sequence types, including HBA CNV and HBB mutations, significantly depend on gender in Xishuangbanna but not in Dehong. With the supportive evidence from previous researches, we accept that some certain mutations depend on gender regionally. This association seems peculiar. It is among one common people on a small geographical scale, while other recorded thalassemia gender difference varies by ethnics and continent.

An Observational Study of the Effect of Hemoglobinopathy, Alpha Thalassemia and Hemoglobin E on P. Vivax Parasitemia

Background

The protective effect of α-thalassemia, a common hematological disorder in Southeast Asia, against Plasmodium falciparum malaria has been well established. However, there is much less understanding of the effect of α-thalassemia against P. vivax. Here, we aimed to investigate the proportion of α-thalassemia including the impact of α-thalassemia and HbE on the parasitemia of P. vivax in Southeast Asian malaria patients in Thailand.

Methods

A total of 210 malaria patients, admitted to the Hospital for Tropical Diseases, Thailand during 2011–2012, consisting of 159 Myanmeses, 13 Karens, 26 Thais, 3 Mons, 3 Laotians, and 6 Cambodians were recruited. Plasmodium spp. and parasite densities were determined. Group of deletion mutation (--^SEA, −α^3.7, −α^4.2deletion) and substitution mutation (HbCS and HbE) were genotyped using multiplex gap-PCR and PCR-RFLP, respectively.

Results

In our malaria patients, 17/210 homozygous and 74/210 heterozygous −α^3.7 deletion were found. Only 3/210 heterozygous −α^4.2 and 2/210 heterozygous--^SEA deletion were detected. HbE is frequently found with 6/210 homozygotes and 35/210 heterozygotes. The most common thalassemia allele frequencies in Myanmar population were −α^3.7 deletion (0.282), followed by HbE (0.101), HbCS (0.013), −α^4.2 deletion (0.009), and --^SEA deletion (0.003). Only density of P. vivax in α-thalassemia trait patients (−α^3.7/−α^3.7, --^SEA/αα, −α^3.7/−α^4.2) but not in silent α-thalassemia (−α^3.7/αα, −α^4.2/αα, αα^CS/αα) were significantly higher compared with non-α-thalassemia patients (p=0.027). HbE did not affect P. vivax parasitemia. The density of P. falciparum significantly increased in heterozygous HbE patients (p=0.046).

Conclusions

Alpha-thalassemia trait is associated with high levels of P. vivax parasitemia in malaria patients in Southeast Asia.

Genetic origin of α0-thalassemia (SEA deletion) in Southeast Asian populations and application to accurate prenatal diagnosis of Hb Bart's hydrops fetalis syndrome

α⁰-thalassemia of SEA deletion (—^SEA) is common among Southeast Asian and Chinese. Using haplotype and phylogenetic analyses, we examined the origin of this defect in Southeast Asian populations. Study was done on both normal and α⁰-thalassemia alleles in 3 ethnic groups including 96 Thai, 52 Laotian and 21 Cambodian. Five SNPs encompassing the (—^SEA) including (rs3760053 T>G), (rs1211375 A>C), (rs3918352 A>G), (rs1203974 A>G) and (rs11248914 C>T) were examined using high-resolution melting assays. It was found that 94.0% of Thai, 100% of Laotian and 100% of Cambodian α⁰-thalassemia alleles were linked to the same haplotype: the haplotype H4 (AAGC), representing an Asian specific origin. An G allele of the (rs3760053) was found to be in strong linkage disequilibrium with the α⁰-thalassemia allele in these populations. A multiplex PCR assay was developed to detect simultaneously the (—^SEA) allele and genotyping of a linked (rs3760053) to improve accuracy of prenatal diagnosis of α⁰-thalassemia. Application of this multiplex PCR assay for routine prenatal diagnosis of α⁰-thalassemia in 12 families revealed a 100% concordant result with conventional gap-PCR assay. Therefore, a single genetic origin is responsible for the spread and high prevalence of the (—^SEA) in the region. The multiplex PCR assay developed should provide a double-check PCR system for more accurate diagnosis and allow the monitoring of possible maternal contamination at prenatal diagnosis of this important genetic disorder.

An international registry of survivors with Hb Bart's hydrops fetalis syndrome

Hemoglobin (Hb) Bart's hydrops fetalis syndrome (BHFS) resulting from α0-thalassemia is considered a universally fatal disorder. However, over the last 3 decades, improvements in intrauterine interventions and perinatal intensive care have resulted in increasing numbers of BHFS survivors. We have initiated an international registry containing information on 69 patients, of which 31 are previously unpublished. In this perspective, we analyze the available clinical information to document the natural history of BHFS. In the future, once we have accrued sufficient cases, we aim to build on this study and provide information to allow counseling of at-risk couples. To date, 39 patients have survived beyond the age of 5 years, 18 of whom are now older than 10 years. Based on the available cases, we find evidence to suggest that intrauterine therapy provides benefits during the perinatal and neonatal period; however, it may not provide additional benefits to long-term growth and neurodevelopmental outcomes. Growth retardation is a major adverse long-term outcome among BHFS patients with ∼40% being severely affected in terms of weight and ∼50% in terms of height. There is also an increased risk of neurodevelopmental delay as we find 20% (11/55) of BHFS survivors suffer from a serious delay of ≥6 months. Most patients in the registry require lifelong transfusion and often have associated congenital abnormalities and comorbidities. This perspective is a first step in gathering information to allow provision of informed counseling on the predicted outcomes of affected babies.

Impact of prematurity and immigration on neonatal screening for sickle cell disease

Background

Others have described a relationship between hemoglobin A levels and gestational age, gender and ethnicity. However, studies are needed to determine normal cut-off points considering these factors. To address this issue we designed a study to determine the percentiles of normality of neonatal hemoglobin A levels taking these factors into account.

Methods

This cross-sectional study involved 16,025 samples for sickle cell disease screening in the province of Alicante, Spain, which has a high immigration rate. The primary variable was hemoglobin A, and the secondary variables were gender, gestational age (preterm and full term) and maternal origin (Spain, the rest of Europe, North Africa, Sub-Saharan Africa, Latin America and Asia). Percentiles of normality (1 and 99) were obtained by origin, gender and gestational age using quantile regression models and bootstrap samples. The association between these percentiles of normality and altered levels (≥1%) of hemoglobin E was analyzed. We obtained the percentiles of normality (1 and 99) for each maternal origin, gender and gestational age.

Results

Of a total of 88 possible E carriers, 65 had above-normal hemoglobin A levels (74%). The levels of normality for hemoglobin A varied greatly according to the maternal origin and gestational age.

Conclusion

With the levels of normality that we established it is possible to discard samples with unrecorded blood transfusions. Our methodology could be applied to other diseases in the neonatal screening.

Sonographic markers of fetal α-thalassemia major

α-Thalassemia prevails in Southeast Asia, where α-thalassemia major is a lethal type. Sonography is a helpful and cost-effective screening tool for detecting α-thalassemia major fetuses. The cardiothoracic ratio, placental thickness, and middle cerebral artery peak systolic velocity are most used in clinical practice. These sensitive markers are helpful for evaluation of the hemodynamic status and cardiovascular function of the affected fetuses. They can predict fetal α-thalassemia major and assess the efficacy of treatment noninvasively; therefore, the medical costs as well as the possibility of fetal loss caused by invasive procedures can be reduced. Other potentially useful sonographic markers need further studies, although previous preliminary research suggests their usefulness. This article will review those sonographic markers.