Fetal Hemoglobin Quantitative Trait Locus 1

A number sign (#) is used with this entry because hereditary persistence of fetal hemoglobin (HPFH) can result from deletions within or encompassing the beta-globin gene cluster (see HBB, 141900) on chromosome 11p15, including deletions that also encompass the delta-globin gene (142000), or from point mutations in the promoter regions of either the HBG1 (142200) or the HBG2 (142250) gene.

Other fetal hemoglobin quantitative trait loci (QTL) include HBFQTL2 (142470) on chromosome 6q23, HBFQTL3 (305435) on chromosome Xp22.2, and HBFQTL5 (142335) on chromosome 2p15, and HBFQTL6 (613566), caused by mutation in the KLF1 gene (600599) on chromosome 19p13. A QTL on chromosome 8q (HBFQTL4; 606789) is thought to interact with the common XmnI-G-gamma polymorphism in HBG2 (142250.0028) to influence the production of HbF.

Description

Classic hereditary persistence of fetal hemoglobin (HPFH) is characterized by a substantial elevation of fetal hemoglobin (HbF) in adult red blood cells. There are no other phenotypic or hematologic manifestations. Expression of the HBG1 and HBG2 genes, which encode the gamma isoforms of HbF, is normally suppressed shortly before birth and replaced by expression of the beta- (HBB; 141900) or delta- (HBD; 142000) chains, which form adult hemoglobin. Adults normally have less than 1% HbF, whereas heterozygotes for HPFH have 5 to 30% HbF. HPFH heterozygotes have essentially normal red cell indices and a rather homogeneous distribution of HbF among red cells, termed 'pancellular.' Homozygotes for HPFH can express HbF in up to 100% of red blood cells (Thein and Craig, 1998).

Delta-beta thalassemia is a hemoglobin disorder characterized by decreased or absent synthesis of the delta- and beta-globin chains with a compensatory increase in expression of fetal gamma-chain synthesis from the affected chromosome. Individuals with delta-beta thalassemia have hypochromic, microcytic anemia and increased HbF, which may mitigate the anemia depending on the level of HbF. Delta-beta thalassemia and some forms of HPFH result from deletions within the beta-globin gene cluster on chromosome 11p15; this has been referred to as 'deletional' HPFH. HPFH can also result from point mutations in the promoter regions of the gamma globulin genes HBG1 and HBG2; this has been referred to as 'non-deletional' HPFH (Ottolenghi et al., 1982; Forget, 1998).

Forget (1998) noted that HPFH and delta-beta thalassemia are not clearly distinct disorders, but rather show partially overlapping features that may defy classification. Higher expression of HbF is often termed 'pancellular,' whereas lower expression of HbF is often termed 'heterocellular,' although these represent a spectrum.

Approximately 10% of the population has HPFH manifest as modest elevations of HbF (1 to 4%) present in a subset of red cells (about 4.5%) termed F cells. This is also sometimes referred to as 'heterocellular' HPFH, and is considered to be a multifactorial trait influenced by multiple genetic loci (Thein and Craig, 1998).

Clinical Features

Conley et al. (1963) reported hereditary persistence of fetal hemoglobin in 79 individuals from 15 African American families. Some individuals had only fetal hemoglobin with glycine-136 (HBG2), whereas others had both glycine-136 and alanine-136 (HBG1) forms of fetal hemoglobin. This trait was thereafter described in Greeks and sporadically in other ethnic groups, e.g., Thais (see bibliography of Wasi et al., 1968). Affected Greeks studied by Wasi et al. (1968) had only fetal hemoglobin of the alanine-136 type (HBG1). The differences were explained on the basis of various deletions involving a region containing several linked hemoglobin genes.

Schokker et al. (1966) reported an association between beta-thalassemia (see 141900) and a high fetal hemoglobin determinant in a pedigree of Dutch origin.

Weatherall et al. (1975) reported a British family in which 13 members had elevated levels of HbF that segregated into 2 groups with mean values of 19.8% and 8.9%, respectively. Genetic data indicated that the individuals in the former group were probably homozygous, and those in the latter group heterozygous, for the gene causing persistent HbF production. Biochemical studies showed that most of the HbF contained gamma-A (HBG1), with a small (10%) amount of the gamma-G (HBG2) in both homozygotes and heterozygotes. Weatherall et al. (1975), who referred to this entity as the 'British' type of HPFH, noted that the condition differed from previously described forms of HPFH by virtue of the heterogeneous distribution of the HbF and the presence of beta and delta-chain synthesis in homozygotes. In the family reported by Weatherall et al. (1975), Tate et al. (1986) identified a mutation in the promoter of the HBG1 gene (142200.0028). This was referred to as a non-deletional form of HPFH due to variation at the beta-globin gene cluster on 11p15. Homozygotes were clinically and hematologically normal except for increased HbF, ranging from 18 to 21%. Heterozygotes had HbF of 3.5 to 10%.

Marinucci et al. (1981) observed a family in southern Italy in which beta-thalassemia was inherited over 3 generations together with a high HbF level (8-12%) and an increased number of F cells. Two individuals who were homozygous for beta-thalassemia had a mild phenotype with hemoglobin consisting mainly of HbF in almost all red cells (pancellular HPFH). Marinucci et al. (1981) noted the considerable clinical benefit of the coexistence of HPFH determinants capable of increasing the size of the F-cell population in patients with homozygous thalassemia.

In a large Australian kindred with nondeletional heterocellular HPFH, Donald et al. (1988) found that fetal hemoglobin was increased to values between 1.8 and 7.9% in 13 members. HbF was composed predominantly of gamma-A chains, and the phenotype was closely linked to the beta-globin gene cluster.

Bhardwaj et al. (2003) described a black female who was identified by newborn screening as having sickle cell disease (603903) with a carrier father and a mother without sickle trait. At 11 months, the child had microcytosis and borderline anemia with a high hemoglobin F (45%); the mother was found to have an elevated HbF (32.1%) consistent with being a carrier of HPFH. Subsequent molecular analysis with a specialized gap-PCR technique determined that both mother and daughter were heterozygous for a deletion in the HBB gene cluster.

Mapping

Among several families with either sickle cell anemia or beta-thalassemia who also showed segregation of HPFH, Wood et al. (1976) found close linkage between the HPFH gene and the beta-globin gene on chromosome 11p15. The findings suggested that the HPFH locus in these families was identical to or closely related to the regulatory region for gamma-globin synthesis. The frequency of F cells was particularly high among those patients with beta-thalassemia and sickle cell anemia, consistent with preferential survival of F cells in bone marrow and peripheral blood.

Marinucci et al. (1981) found linkage to the beta-globin locus on chromosome 11p15 in an Italian family with beta-thalassemia and HPFH.

Dover et al. (1981) amassed 3 lines of evidence that a locus regulating generation of F cells was linked to the gamma-delta-beta complex. (1) The percentages of F reticulocytes, while widely divergent in the population of homozygous sickle cell patients, showed a correlation coefficient of 0.94 in homozygous sib pairs (correlation coefficient for within-person percentages for successive samples = 0.95). (2) Mid-parental F-cell levels in healthy heterozygous parents, while well within the normal adult range of 0.2 to 10%, correlated well (r = 0.92) with the percentage of F reticulocytes produced by their homozygous offspring. (3) In the isolated population of eastern Saudi Arabia the coefficient of variation for F-reticulocyte level in homozygous sickle persons is about 25% (not greatly different from the average coefficient of 23% for variation between sibs). On the other hand, in the outcrossed American Black population, the coefficient of variation is 66%. The Saudi population may be homozygous at the F-cell regulatory locus. Specifically, the Saudi homozygous patients have a high F-cell percentage. If American Blacks with sickle cell anemia and elevated percentages of F reticulocytes likewise are homozygotes, the frequency of the gene can be calculated as 0.35. There is other evidence that HbF and F-cell levels are genetically determined in baboon (DeSimone et al., 1980) and in man (Zago et al., 1979), both anemic and nonanemic.

Boyer and Dover (1982) referred to 6 recombinants out of 39 opportunities for the linkage between F-cell production and the beta-globin locus. Boyer (1983) set the limits as 0.12 and 0.23 for the true recombination fraction for beta-globin and F-cell production.

Old et al. (1982) reported a family with HPFH in whom linkage analysis showed that the regulatory gene was close to or coincident with the beta-globin complex on chromosome 11.

Efremov et al. (1987) characterized the haplotype associated with heterocellular HPFH in Yugoslavia. The trait was associated with a chromosome 11p15 whose restriction enzyme haplotype was identical to that observed in African patients with sickle cell anemia.

Heterogeneity

Martinez and Colombo (1974) reported a family of African origin in which HPFH occurred at a level of 5% HbF. Linkage analysis showed that the gene did not behave as an allele of the beta-globin complex, although the possibility of a crossover between the gamma and the beta loci could not be excluded. The authors suggested that a diffusible factor might regulate gamma-chain synthesis. In a follow-up of the family reported by Martinez and Colombo (1974), Martinez et al. (1989) demonstrated that a determinant for HPFH segregated independently from the beta-globin gene cluster on 11p15.

Soummer et al. (1981) reported a family of Algerian origin in which a father and daughter, the proposita, had both beta-thalassemia and HPFH. HbF levels were 3.6% and 6.15%, respectively, and 16% and 19% F cells, respectively. Two additional daughters had only HPFH, with HbF levels of 1.83% and 2.69%, respectively, and 12% and 17% F cells, respectively. A daughter of the proposita had only beta-thalassemia, with HbF level of 1.4% and F cell number of 8%. Soummer et al. (1981) concluded that the father of the 3 daughters carried both genes for beta-thalassemia and HPFH, and transmitted both genes to the proposita, but only the HPFH gene to the other 2 daughters. The findings indicated that the 2 traits were unlinked, suggesting that a locus distinct from the beta-globin cluster is responsible for HPFH in this family.

Gianni et al. (1983) reported a Sardinian family in which a homozygous beta-thalassemic patient had an unusually mild form of the disease, which was ascribed to the coexistence of a gene causing heterocellular HPFH. Four family members had heterozygous beta-thalassemia with HPFH, and 5 had HPFH without beta-thalassemia. Linkage analysis using restriction polymorphisms indicated that HPFH in this family was not linked to the beta-globin gene cluster. Gianni et al. (1983) postulated that the putative gene may code for a diffusible substance acting, directly or indirectly, on gamma-globin gene expression.

Giampaolo et al. (1984) concluded that the HPFH mutation lies outside the gamma-delta-beta-globin DNA segment on 11p15. They observed independent segregation of HPFH and beta-thalassemia trait in 2 families, 1 of which showed no segregation of DNA polymorphisms within the segment when HPFH and beta-thalassemia segregated. By the coexistence of a polymorphic variant of the A-gamma chain (gamma-T), they were also able to demonstrate that the increased gamma-chain synthesis caused by the heterocellular HPFH determinant was directed by both chromosomes. This finding was in contrast to delta-beta thalassemia and pancellular HPFH, in which only the chromosomes carrying the mutation are affected via a cis effect.

The frequency of F cells in sickle cell disease can range from 2 to 50%. By studying 59 sib pairs with sickle cell anemia from Jamaica and the US, Boyer et al. (1984) provided evidence for at least 1 locus distinct from the beta-globin locus that is important for the regulation of F-cell production.

In a large family originating from northern India with heterocellular hereditary persistence of fetal hemoglobin, Sampietro and Thein (1991) demonstrated linkage to a polymorphic locus at 7q36, with a maximum lod score of 2.8 at a recombination fraction of 0.09 when their data were combined with those from a second pedigree of Italian origin. The propositus in the Indian family, despite being homozygous for beta-thalassemia and unable to produce any normal adult hemoglobin, had exceedingly mild clinical disease because of coinheritance of heterocellular HPFH.

Molecular Genetics

Deletions in Chromosome 11p15

Kan et al. (1975) identified deletions in the delta and beta HB loci in individuals with increased HbF.

Bernards and Flavell (1980) mapped the beta-like globin region in 2 HPFH patients: an African American who was homozygous for both G-gamma and A-gamma HbF expression, and a Greek who was heterozygous for A-gamma expression. In the first individual, there was a 24-kb deletion in the hemoglobin gene region that removed the gamma-, delta-, and beta-globin genes. The 5-prime break was situated about 9 kb upstream from the delta gene and the 3-prime break at least 7 kb past the beta gene. No deletion was detected in the heterozygous Greek.

Ottolenghi et al. (1982) studied 3 Mediterranean families with delta-beta thalassemia and 1 Southern Italian family with HPFH using restriction enzyme mapping and expression of gamma-A and gamma-G. There was molecular heterogeneity of deletion sizes at the beta-globin locus: Sicilian and Calabrian delta-beta thalassemia patients showed a deletion starting from the delta-globin intron and ending several kilobases 3-prime to the beta-globin gene. In a Spanish family with thalassemia, the deletion started 2 to 3 kb 5-prime to the delta-globin gene and extended well beyond the beta-globin gene. In addition, the Spanish family was found to have a variant of gamma-A fetal hemoglobin (142200.0001) which accounted for all of the gamma-A production in heterozygotes. These findings indicated that persistent production of gamma chains occurred in cis to the delta-beta gene deletion. Comparison with the deletions in HPFH suggested that deletion of a region about 3.5 kb 5-prime to the delta gene may be critical to the persistent expression of high levels of fetal hemoglobin.

Tuan et al. (1983) found that the deletion in 2 types of HPFH was more extensive than that in 2 types of delta-beta thalassemia. In the former, the 3-prime end of the deletion was about 52 and 57 kb from the 3-prime end of the beta-globin gene; in the latter, the 3-prime end of the deletion was about 5 and 10 kb from the 3-prime end of the beta-globin gene. Thus, the extent of the deletion and the nature of the DNA that is consequently brought into proximity with the gamma-globin genes may be more important in determining the phenotype in these disorders than the nature of the deleted DNA.

Collins et al. (1986) pointed out that the total length of the deleted DNA in 'type 1' and 'type 2' HPFH is nearly the same. Type 1 HPFH is the most common deletion form occurring in African Americans, and type 2 HPFH is the most common form occurring in Ghana. There is an Indian variety which has about half as long a deletion. Collins et al. (1986) speculated that the deleted segment may represent one loop of DNA between 2 attachment sites in the nuclear matrix.

In the Vietnamese G-gamma/A-gamma HPFH, Motum et al. (1993) demonstrated a novel 30-kb deletion located downstream from the beta-globin gene cluster. They compared the sites of the 5-prime and 3-prime breakpoints of this deletion with those for other HPFH-producing deletions downstream from the HBB gene.

De Andrade et al. (2006) used suppressive subtractive hybridization to analyze differential gene expression in a patient with HPFH type 2, the Sicilian form of delta-beta-thalassemia, and normal reticulocytes. HPFH type 2, the Ghanaian form, is caused by a 100-kb deletion at 11p15 that completely removes the delta- and beta-globin genes, with the 3-prime breakpoint near an enhancer element downstream of the beta-globin cluster. Several genes were altered in HPFH and delta-beta-thalassemia compared to normal reticulocytes, including SLC25A37 (610387) and ZHX2 (609185). HBA1 (141800) was also decreased in both conditions compared to normal. The findings suggested an integrated model, including both cis and trans elements, to explain increased Hb-gamma expression in these conditions.

Sankaran et al. (2011) identified 3 families with unusual patterns of hemoglobin expression, suggestive of deletions in the locus of the beta-globin gene. The authors used array comparative genomic hybridization to map the deletions and confirmed breakpoints by PCR assays and DNA sequencing. They found a novel delta-beta-0-thalassemia deletion and a rare HPFH deletion with identical downstream breakpoints. Comparison of the 2 deletions resulted in the identification of a small intergenic region required for gamma-globin gene (HBG1; 142200) silencing. Sankaran et al. (2011) mapped a Kurdish beta-0-thalassemia deletion, which retained the required intergenic region, deleted other surrounding sequences, and maintained fetal hemoglobin silencing. By comparing these deletions and other previously mapped deletions, Sankaran et al. (2011) elucidated a 3.5-kb intergenic region near the 5-prime end of the delta-globin gene that is necessary for gamma-globin silencing. They also found that BCL11A (606557) and its partners bind within this region in the chromatin of adult erythroid cells.

Point Mutations In or Near the HBG1 and HBG2 Genes

Balsley et al. (1982) reported an African American mother and child with gamma-G (HBG2), beta-globin-positive HPFH. The affected chromosome in these persons directed the production of G gamma-chains and beta-chains, but not gamma-A (HBG1) chains. DNA analysis with several restriction enzymes did not detect any deletions in the beta-globin gene cluster region.

Papayannopoulou et al. (1982) noted that the 'Greek' form of HPFH shows HbF predominantly of the gamma-A type. However, cell culture studies of Greek HPFH erythrocytes showed that both gamma genes could be expressed. Restriction endonuclease mapping indicated that the gamma-G, delta, and beta genes in cis to the Greek HPFH determinant were intact and there was no large deletion. This was in contrast to other forms of HPFH which had been associated with large deletions. Papayannopoulou et al. (1982) speculated that the genetic lesion may reside in regulatory sequences that control the level of gamma-A and gamma-G expression. Collins et al. (1985) determined that the Greek form of HPFH was due to a -117G-A SNP in the promoter region of the HBG1 gene (142200.0026).

Farquhar et al. (1983) performed restriction enzyme mapping of the beta-globin cluster in 2 forms of HPFH and could demonstrate no deletion or other abnormality. They suggested that if the DNA structure of the gamma-delta-beta region was indeed normal, these variants could be due to mutations of regulatory loci at sites outside this genomic region.

Fetal Hb levels are influenced by single-nucleotide polymorphisms in the promoter regions of the HBG1 and HBG2 genes, which affect gene expression. Single-base changes influencing hereditary persistence of HbF in the HBG2 gene include -202C-G (142250.0026) (Collins et al., 1984), -175T-C (142250.0027) (Huang et al., 1987), and -158C-T (rs7482144; 142250.0028) (Miller et al., 1987). Single base changes responsible for HPFH in the HBG1 gene include -117G-A (142200.0026) (Collins et al., 1985) and -196C-T (142200.0027) (Gelinas et al., 1986). Several findings indicate that these substitutions cause the HPFH phenotype: (1) only the mutated gene is affected; (2) the substitutions are the only nonpolymorphic deviations from the normal sequence over a large region; and (3) there is a strong correlation between the base substitution and HPFH (Carlson and Ross, 1986).

In a cohort of 1,275 African Americans with sickle cell disease, Lettre et al. (2008) found a significant association between HbF levels and SNP rs7482144 in the HBG2 gene (142250.0028) (p = 4 x 10(-7)), which explained 2.2% of the variation in HbF levels. The association with rs7482144 could not be tested in a Brazilian cohort because the variant was monomorphic in this population.

To fine map HbF association signals, Galarneau et al. (2010) resequenced 175.2 kb from the BCL11A (606557), HBS1L-MYB (612450-189990), and beta-globin loci (representing HBFQTL5 (142335), HBFQTL2 (142470), and HBFQTL1, respectively) in 190 individuals including the HapMap European CEU and Nigerian YRI founders and 70 African Americans with sickle cell anemia. The authors discovered 1,489 sequence variants, including 910 previously unreported variants. Using this information and data from HapMap, Galarneau et al. (2010) selected and genotyped 95 SNPs, including 43 at the beta-globin locus, in 1,032 African Americans with sickle cell anemia. An XmnI polymorphism (rs7482144) in the proximal promoter of HBG2 marks the Senegal and Arab-Indian haplotypes and is associated with HbF levels in African Americans with sickle cell disease (Lettre et al., 2008). Galarneau et al. (2010) replicated the association between rs7482144 and HbF levels (p = 3.7 x 10(-7)). However, rs10128556, a T/C SNP located downstream of HBG1, was more strongly associated with HbF levels than rs7482144 by 2 orders of magnitude (p = 1.3 x 10(-9)). When conditioned on rs10128556, the HbF association result for rs7482144 was not significant, indicating that rs7482144 is not a causal variant for HbF levels in African Americans with sickle cell anemia. The results of a haplotype analysis of the 43 SNPs in the beta-globin locus using rs10128556 as a covariate were not significant (p = 0.40), indicating that rs10128556 or a marker in linkage disequilibrium with it is the principal HbF-influencing variant at the beta-globin locus in African Americans with sickle cell anemia.

Population Genetics

Boyer and Dover (1982) calculated a frequency of about 0.35 for the gene responsible for increased F-cell levels in African Americans.

Nomenclature

HPFH has been characterized by quantifications of HbF fractions and analysis of globin chains. The types of gamma chains, gamma-A or gamma-G, synthesized in HPFH carriers allowed the distinction of mutants with expression of one or both gamma chains, as well as variable expression of the beta and delta genes in cis. For example, 'gamma-G, delta, beta-positive HPFH' or 'gamma-A, gamma-G, delta, beta-negative HPFH' (Farquhar et al., 1983).

History

In a case of a nondeletion form of Sicilian beta-0 hereditary persistence of fetal hemoglobin, Ragusa et al. (1989) found 3 nucleotide variations in the putative enhancer 3-prime to the A-gamma gene, identical to those observed in a case of Seattle HPFH (Gelinas et al., 1988). They concluded, however, that these variations were not responsible for the increased fetal hemoglobin expression since they were found in another patient homozygous for the same haplotype who did not have excessive fetal hemoglobin production.