Insights into genomic structure and evolutionary processes of coastal Suaeda species in East Asia using cpDNA, nDNA, and genome-wide SNPs

Species in the genus Suaeda have few diagnostic characters and substantial morphological plasticity. Hence, regional floras do not provide clear taxonomic information for Suaeda spp. in East Asia. In order to assess the taxonomy of four species in the genus Suaeda (S. australis, S. maritima, S. japonica, and S. heteroptera), cpDNA (rpl32-trnL and trnH-psbA), nDNA (ITS), and MIG-seq analyses were carried out. Genome-wide SNP results indicated three lineages: (1) S. australis in Korea and S. maritima in Japan, (2) S. maritima in Korea and S. heteroptera in China, and (3) S. japionica. In phylogenetic trees and genotype analyses, cpDNA and nDNA results showed discrepancies, while S. japonica and S. maritima in Korea, and S. heteroptera in China shared the same haplotype and ribotype. We suggest that the shared haplotype may be due to chloroplast capture. Based on our results, we assume that S. japonica was formed by homoploid hybrid speciation between the two lineages.

Population genetics of the Manila clam (Ruditapes philippinarum) in East Asia

The Manila clam Ruditapes philippinarum is the world’s second most important bivalve mollusk commercially farmed, whose indigenous populations are mainly distributed in the coastal areas of East Asia. However, with the development of commercialization, mixture of populations and loss of local germplasm have become prominent problems. Here, genetic differentiation of seven Manila clam populations from East Asia was investigated through analyzing the polymorphism of the mitochondrial cytochrome C oxidase subunit I (COI) gene as well as 20 simple sequence repeat (SSR) molecular loci. In total, 40 haplotypes were identified, among which 31 were unique. Moreover, two main haplotypes were detected with several radiating derived haplotypes. Populations in Japan-North Korea shared haplotype Hap_31, and populations in China shared haplotype Hap_7, suggesting that the natural geographical isolation of the Yangtze River and the Yalu River might have divided the East Asian indigenous populations into three groups, which were located in South China, North China, and Japan-North Korea, respectively. The Aquaculture breeding activities from South to North in China might have promoted gene exchange among Manila clam populations. Population in Laizhou had the highest genetic diversity and therefore could be an excellent germplasm source.

The GBA p.G85E mutation in Korean patients with non-neuronopathic Gaucher disease: founder and neuroprotective effects

Background Gaucher disease (GD) is caused by a deficiency of β-glucocerebrosidase, encoded by GBA. Haplotype analyses previously demonstrated founder effects for particular GBA mutations in Ashkenazi Jewish and French-Canadian populations. This study aimed to investigate the clinical characteristics and mutation spectrum of GBA in Korean GD patients and to identify founder effect of GBA p.G85E in non-neuronopathic GD patients. Results The study cohort included 62 GD patients from 58 unrelated families. Among them, 18 patients from 17 families harbored the p.G85E mutation. Haplotype analysis was performed for 9 probands and their parents for whom DNA samples were available. In 58 unrelated probands, the GBA mutation p.L483P was the most common (30/116 alleles, 26%), followed by p.G85E (16%), p.F252I (13%), and p.R296Q (9%). The median age at diagnosis of the 18 patients harboring the p.G85E mutation was 3.8 (range 1.2–57) years. No patients developed neurological symptoms during follow-up periods of 2.2–20.3 (median 13.9) years. The size of the shared haplotype containing GBA p.G85E was 732 kbp, leading to an estimated age of 3075 years. Conclusion The GBA p.G85E mutation, which appears to be neuroprotective despite producing distinctive visceromegaly and skeletal symptoms, exhibited a potential founder effect in Korean GD patients.

The GBA p.G85E mutation in Korean patients with non-neuronopathic Gaucher disease: founder and neuroprotective effects

Background Gaucher disease (GD) is caused by a deficiency of β-glucocerebrosidase, encoded by GBA. Haplotype analyses previously demonstrated founder effects for particular GBA mutations in Ashkenazi Jewish and French-Canadian populations. This study aimed to investigate the clinical characteristics and mutation spectrum of GBA in Korean GD patients and to identify founder effect of GBA p.G85E in non-neuronopathic GD patients. Results The study cohort included 62 GD patients from 58 unrelated families. Among them, 18 patients from 17 families harbored the p.G85E mutation. Haplotype analysis was performed for 9 probands and their parents for whom DNA samples were available. In 58 unrelated probands, the GBA mutation p.L483P was the most common (30/116 alleles, 26%), followed by p.G85E (16%), p.F252I (13%), and p.R296Q (9%). The median age at diagnosis of the 18 patients harboring the p.G85E mutation was 3.8 (range 1.2–57) years. No patients developed neurological symptoms during follow-up periods of 2.2–20.3 (median 13.9) years. The size of the shared haplotype containing GBA p.G85E was 732 kbp, leading to an estimated age of 3,075 years. ConclusionThe GBA p.G85E mutation, which appears to be neuroprotective despite producing distinctive visceromegaly and skeletal symptoms, exhibited a potential founder effect in Korean GD patients.

The GBA p.G85E mutation in Korean patients with non-neuronopathic Gaucher disease: founder and neuroprotective effects

Background Gaucher disease (GD) is caused by a deficiency of β-glucocerebrosidase, encoded by GBA. Haplotype analyses previously demonstrated founder effects for particular GBA mutations in Ashkenazi Jewish and French-Canadian populations. This study aimed to investigate the clinical characteristics and mutation spectrum of GBA in Korean GD patients and to identify founder effect of GBA p.G85E in non-neuronopathic GD patients. Results The study cohort included 63 GD patients from 58 unrelated families. Among them, 18 patients from 17 families harboured the p.G85E mutation. Haplotype analysis was performed for 9 probands and their parents for whom DNA samples were available. In 58 unrelated probands, the GBA mutation p.L483P was the most common (30/116 alleles, 26%), followed by p.G85E (16%), p.F252I (13%), and p.R296Q (10%). Of the 18 patients harbouring the p.G85E mutation, their median age at diagnosis was 3.8 (range 1.2–57) years. No patients developed neurological symptoms during follow-up periods of 2.2–20.3 (median 13.9) years. The size of the shared haplotype containing GBA p.G85E was 732 kbp, leading to an estimated age of 3,075 years. Conclusion The GBA p.G85E mutation, which appears to be neuroprotective despite producing distinctive visceromegaly and skeletal symptoms, exhibited a potential founder effect in Korean GD patients.

Identifying non-identical-by-descent rare variants in population-scale whole genome sequencing data

The site frequency spectrum in human populations is not accurately modeled by an infinite sites model, which assumes that all mutations are unique. Despite the pervasiveness of recurrent mutations, we lack computational methods to identify these events at specific sites in population sequencing data. Rare alleles that are identical-by-descent (IBD) are expected to segregate on a long, shared haplotype background that descends from a common ancestor. However, alleles introduced by recurrent mutation or by non-crossover gene conversions are identical-by-state and will have a shorter expected shared haplotype background. We hypothesized that the expected difference in shared haplotype background length can distinguish IBD and non-IBD variants in population sequencing data without pedigree information. We implemented a Bayesian hierarchical model and used Gibbs sampling to estimate the posterior probability of IBD state for rare variants, using simulations to demonstrate that our approach accurately distinguishes rare IBD and non-IBD variants. Applying our method to whole genome sequencing data from 3,621 individuals in the UK10K consortium, we found that non-IBD variants correlated with higher local mutation rates and genomic features like replication timing. Using a heuristic to categorize non-IBD variants as gene conversions or recurrent mutations, we found that potential gene conversions had expected properties such as enriched local GC content. By identifying recurrent mutations, we can better understand the spectrum of recent mutations in human populations, a source of genetic variation driving evolution and a key factor in understanding recent demographic history.

Undocumented translocations spawn taxonomic inflation in Sri Lankan fire rasboras (Actinopterygii, Cyprinidae)

A recent (2013) taxonomic review of the freshwater-fish genus Rasboroides, which is endemic to Sri Lanka, showed it to comprise four species: R. vaterifloris, R. nigromarginatus, R. pallidus and R. rohani. Here, using an integrative-taxonomic analysis of morphometry, meristics and mitochondrial DNA sequences of cytochrome b (cytb) and cytochrome oxidase subunit 1 (coi), we show that R. nigromarginatus is a synonym of R. vaterifloris, and that R. rohani is a synonym of R. pallidus. The creation and recognition of unnecessary taxa (‘taxonomic inflation’) was in this case a result of selective sampling confounded by a disregard of allometry. The population referred to R. rohani in the Walawe river basin represents an undocumented trans-basin translocation of R. pallidus, and a translocation into the Mahaweli river of R. vaterifloris, documented to have occurred ca 1980, in fact involves R. pallidus. A shared haplotype suggests the latter introduction was likely made from the Bentara river basin and not from the Kelani, as claimed. To stabilize the taxonomy of these fishes, the two valid species, R. vaterifloris and R. pallidus, are diagnosed and redescribed, and their distributions delineated. We draw attention to the wasteful diversion of conservation resources to populations resulting from undocumented translocations and to taxa resulting from taxonomic inflation. We argue against translocations except where mandated by a conservation emergency, and even then, only when supported by accurate documentation.

Chuvash Polycythemia Patients from Afghanistan and Southern India Share a Common VHL Gene Haplotype. Support for Its Origin before Asians and Europeans Diverged

Chuvash polycythemia is a rare autosomal recessive hereditary disease, with affected homozygotes having decreased survival mainly because of increased incidence of stroke and other thrombotic complications. Intriguingly this risk may be augmented, rather than ameliorated, by phlebotomies (Sergueeva et al, Blood, 2015, and Haematologica 2017). Chuvash polycythemia is characterized by a C to T missense mutation of the von Hippel Lindau (VHL) gene at nucleotide 589 (VHLC589T, encoding VHLR200W). VHL is a negative regulator of hypoxia-inducible factor (HIF) α subunits. Homozygosity for VHLC589T upregulates hypoxic responses through constitutively augmented HIF signaling even in normoxia, resulting in an increase of erythropoiesis. Heterozygosity leads to only mild augmentation of hypoxia sensing. Chuvash polycythemia was first identified in people of the Chuvash region in Russia, where it has estimated heterozygosity frequency of 1.7%, likely due to a founder effect. The incidence of Chuvash polycythemia elsewhere is sporadic, and the condition is found in other ethnic groups, including northern Indians of Indo-European ethnicity and northern Europeans. Another hot spot of gene frequency was found among Italians on the island of Ischia. We previously published that VHLC589Thomozygotes from various parts of the world share a common VHL haplotype, and from the size of the shared haplotype, we could calculate that it originated from the same founder about 30-50,000 years ago (Liu, et al, Blood 2004). The same shared haplotype was also identified in Ischia in VHLC589Thomozygotes (Perrotta et al, Blood 2006). A single individual from Turkey had the VHLC589T mutation on a different haplotype (Turkish haplotype, Cario, et al, Heamatologica, 2005) demonstrating the existence of another independent founder of the VHLC589T mutation. Two polycythemic patients with VHLC589T mutation were recently referred to us, one from Afghanistan (among people using the Dravidian language who had frequent historical interactions with Turkey) and the other from southern India (the ethnicity of which is also Dravidian and distinct from Indo-European ethnicity). We hypothesized that the Chuvash polycythemia patients, who originated from Afghanistan and Southern India, might have the Turkish haplotype, strengthening support for two independent founders of this haplotype. We analyzed the VHL haplotype of these 2 individuals using 6 selected single nucleotide polymorphisms. Genomic DNA was isolated from granulocytes. Haplotype analysis was performed by Sanger Sequencing. We found that the Chuvash polycythemia patients from Afghanistan and Southern India shared the common Chuvash haplotype (Table). We conclude that the Chuvash haplotype is also present in VHLC589T homozygotes in Afghanistan and Southern India, suggesting that the VHLC589T mutation in these areas arose from the same common founder. The data support the notion that the Chuvash polycythemia VHL mutation originated relatively early in modern human evolution- possibly after humans moved from Africa- as it is present in different ethnic and racial groups (Europeans and Asians). This observation is compatible with the notion that VHLC589T heterozygosity provides some evolutionary advantage (present in various ethnic groups and did not disappear, i.e., absence of negative selection because of increased mortality of homozygotes). It has been shown that heterozygosity for VHLC589T provides some protection from anemia; it is likely that other evolutionary benefits remain to be identified (Miasnikova et al, Haematologica 2011). Yet, such an advantage is very mild (very low gene frequency worldwide of this mutation). These data provide additional evidence that support a VHLC589T origin before Asians and European diverged. Disclosures No relevant conflicts of interest to declare.

Population Structure of Pseudocercospora fijiensis in Costa Rica Reveals Shared Haplotype Diversity with Southeast Asian Populations

Pseudocercospora fijiensis is the causal pathogen of black Sigatoka, a devastating disease of banana that can cause 20 to 80% yield loss in the absence of fungicides in banana crops. The genetic structure of populations of P. fijiensis in Costa Rica was examined and compared with Honduran and global populations to better understand migration patterns and inform management strategies. In total, 118 isolates of P. fijiensis collected from Costa Rica and Honduras from 2010 to 2014 were analyzed using multilocus genotyping of six loci and compared with a previously published global dataset of populations of P. fijiensis. The Costa Rican and Honduran populations shared haplotype diversity with haplotypes from Southeast Asia, Oceania, and the Americas but not Africa for all but one of the six loci studied. Gene flow and shared haplotype diversity was found in Honduran and Costa Rican populations of the pathogen. The data indicate that the haplotypic diversity observed in Costa Rican populations of P. fijiensis is derived from dispersal from initial outbreak sources in Honduras and admixtures between genetically differentiated sources from Southeast Asia, Oceania, and the Americas.

Second Blood or Marrow Transplant (BMT) for Relapse: Mismatch Haplotype Switch May Improve Outcome

Introduction: With improvements in supportive care, including graft-versus-host disease (GVHD) control, relapse has become the major complication of allogeneic BMT. The use of haploidentical donors often allows the potential to select a different donor for the second transplant. We examined the outcomes of patients who underwent a second BMT for relapse at Johns Hopkins between 2005 and 2014. We hypothesized that if loss of heterozygosity is a mechanism for relapse after haploBMT, then utilizing a donor that recognizes the other shared haplotype could improve antitumor activity and thus overall survival (OS). In the case of a failed matched transplant, recognition of a non-shared haplotype on the tumor by the second allograft would be beneficial. Methods: We identified all patients who received a second transplant for relapse of a hematologic malignancy between 2005 and 2014. Acute GVHD (aGVHD) is reported as Glucksberg grades 1-4; chronic GVHD (cGVHD) is reported as limited or extensive. GVHD and non-relapse mortality (NRM) was calculated via cumulative incidence (CI) with competing risk analysis. OS was calculated as the time from second transplant to death or last known follow-up and estimated using the Kaplan Meier method. Differences in time to death between patient groups were estimated using Cox proportional hazards models. Non-relapse mortality was estimated using Fine and GrayÕs method. Results: Between 2005 and 2014, 40 patients received a second BMT for a relapsed hematologic malignancy (Table 1). The median age at second transplant was 43.9 (range 1 to 74); 14 (35%) were female. Fifteen (41%) received myeloablative conditioning for their first transplant, and 35 (92%) received high dose post-transplant cyclophosphamide (PTCy) as part of their GVHD prophylaxis. The incidence of grade 2-4 aGVHD after the first transplant was 13%, and limited cGVHD was 13%. There was no extensive cGVHD. Re-induction therapy and second allograft characteristics (Table 2): Refractory or progressive disease at the time of second transplant was present in 20% of patients, and 7/40 (18%) had their second transplant within 1 year. After a first failed HLA-matched transplant, 15 received a haploidentical graft, and 4 received a second HLA-matched graft. Among the 21 who relapsed after a haploBMT, 7 received an HLA-matched allograft, and 14 received a haploidentical graft; 6 out of those 14 used a donor that switched the shared haplotype. Most (81%) received PTCy with the second BMT. Median follow up is 598 days. Median OS in the cohort is 911 days (95% CI 602 Ð NR); 4 year OS is 38%. The CI of NRM by 2 years was 29% - 4 patients died of complications of GVHD (only one of whom received post-transplant Cyclophosphamide), 3 associated with prolonged cytopenias, 1 within a month of BMT, and 3 of pneumonia. Grade 2-4 aGVHD occurred in 11 pts (28%), grade 3-4 in 5 (13%). Extensive cGVHD was seen in 7 (18%). Median OS for the patients who relapsed after initial haploBMT who were then retransplanted with an HLA-haploidentical donor with a different shared haplotype has not been reached, versus a median OS of 501 [317-2950+] days among the 15 who did not receive a graft with an alternate shared haplotype (HR 0.21 [0.03, 1.61]; p=0.06). If the 19 patients who received a matched allograft at first transplant are included, median OS is 552 days in the group transplanted with a second graft with the same shared haplotype(s), and 1308 days (Figure 1) in the group whose allograft contained a different non-shared haplotype (HR 0.39 [0.16, 0.98]; p=0.04). OS was better when the second transplant was performed more than one year after the first (HR 0.30 [0.11, 0.80]; p=0.03). A trend towards improved OS was associated with disease status at time of second transplant (remission or chemo-responsiveness versus progressive or refractory disease; HR 0.41 [0.16, 1.03]; p=0.07). Source of graft (BM versus peripheral), conditioning intensity, era of transplant (2005-2010 versus 2010-2015), same versus different donor, and age group (<25, 25-60, 60+) did not significantly influence OS. Conclusion: Second transplants are feasible in all age groups and provide a reasonable chance of long-term survival. GVHD rates using PTCy are low, and similar to that seen with first BMTs. An allograft sharing a different haplotype in the case of relapse after haploBMT, or a haploidentical donor after failure of a matched graft, may be beneficial. OS by Second Donor Haplotype OS by Second Donor Haplotype Figure 1 Figure 1. Disclosures Brodsky: Apellis Pharmaceuticals Inc: Membership on an entity's Board of Directors or advisory committees; Alexion Pharmaceuticals Inc: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Achillion Pharmaceuticals: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees.