[Analysis of Thalassemia Gene Carriers in 19 482 Pregnant Women from 2015 to 2019 in Guilin, Guangxi].

OBJECTIVE: To investigate the types and frequencies of thalassemia genes carried by the pregnant women in Guilin, Guangxi Zhuang Autonomous Region, China. METHODS: From January 2015 to December 2019, blood samples of the pregnant women who visited the Outpatients of Obstetrics clinic and Eugenics Genetic clinic in Affiliated Hospital of Guilin Medical University were collected. Gap-PCR was used to detect deletional α-thalassemia, PCR-RDB to detect the gene mutations of non-deletional α-thalassemia and ß-thalassemia, and MLPA or DNA sequencing to detect rare thalassemia mutations. Different types and frequencies of thalassemia mutations carried by pregnant women were analyzed statistically. RESULTS: A total of 19 482 blood samples were collected, including 3 801 thalassemia gene carriers (19.51%). Seven types of α-thalassemia gene mutation were detected with a carrier rate of 15.43%. Among them, --SEA deletion (7.32%), -α3.7 deletion (3.97%), and -α4.2 deletion (1.4%) were the commonest types. Twelve types of ß-thalassemia mutations were detected with a carrier rate of 5.02%. Among them, CD41-42 (-TCTT) (2.32%), CD17 (AAG>TAG) (1.23%), and IVS-II-654 (C>T) (0.55%) were the commonest types. In addition, 107 cases of rare thalassemia gene mutations and abnormal hemoglobin were found at the same time. CONCLUSION: Guilin is a high-risk area for thalassemia. Alpha-thalassemia is dominated by --SEA deletion, -α3.7 deletion, and -α4.2 deletion, while ß-thalassemia is by CD41-42 (-TCTT), CD17(AAG>TAG), and IVS-II-654(C>T).

Benchmark on Indexing Algorithms for Accelerating Molecular Similarity Search.

Structurally similar analogues of given query compounds can be rapidly retrieved from chemical databases by the molecular similarity search approaches. However, the computational cost associated with the exhaustive similarity search of a large compound database will be quite high. Although the latest indexing algorithms can greatly speed up the search process, they cannot be readily applicable to molecular similarity search problems due to the lack of Tanimoto similarity metric implementation. In this paper, we first implement Python or C++ codes to enable the Tanimoto similarity search via several recent indexing algorithms, such as Hnsw and Onng. Moreover, there are increasing interests in computational communities to develop robust benchmarking systems to access the performance of various computational algorithms. Here, we provide a benchmark to evaluate the molecular similarity searching performance of these recent indexing algorithms. To avoid the potential package dependency issues, two separate benchmarks are built based on currently popular container technologies, Docker and Singularity. The Singularity container is a rather new container framework specifically designed for the high-performance computing (HPC) platform and does not need the privileged permissions or the separated daemon process. Both benchmarking methods are extensible to incorporate other new indexing algorithms, benchmarking data sets, and different customized parameter settings. Our results demonstrate that the graph-based methods, such as Hnsw and Onng, consistently achieve the best trade-off between searching effectiveness and searching efficiencies. The source code of the entire benchmark systems can be downloaded from https://github.uconn.edu/mldrugdiscovery/MssBenchmark.

On the VC-Dimension of Unique Round-Trip Shortest Path Systems.

The VC-dimension, which has wide uses in learning theory, has been used in the analysis and design of graph algorithms recently. In this paper, we study the problem of bounding the VC-dimension of unique round-trip shortest path set systems (URTSP), which are set systems induced by sets of vertices in unique round-trip shortest paths in directed graphs. We first show that different from the VC-dimensions of set systems induced by unique undirected and directed shortest paths in undirected and directed graphs respectively, the VC-dimension of URTSP can be larger than 3. We then prove that the VC-dimension of URTSP is at most 32. Furthermore, we apply the VC-dimension result to the minimum k-round-trip shortest path cover problem (k-RTSPC), which is to find for a directed graph a minimum vertex set to intersect every round-trip shortest path containing at least k vertices, and derive an upper bound on the size of the vertex set. The k-RTSPC problem can be useful in many real-world applications, including optimal placement of facilities.

Improved Dynamic Graph Learning through Fault-Tolerant Sparsification.

Graph sparsification has been used to improve the computational cost of learning over graphs, e.g., Laplacian-regularized estimation, graph semisupervised learning (SSL) and spectral clustering (SC). However, when graphs vary over time, repeated sparsification requires polynomial order computational cost per update. We propose a new type of graph sparsification namely fault-tolerant (FT) sparsification to significantly reduce the cost to only a constant. Then the computational cost of subsequent graph learning tasks can be significantly improved with limited loss in their accuracy. In particular, we give theoretical analysis to upper bound the loss in the accuracy of the subsequent Laplacian-regularized estimation, graph SSL and SC, due to the FT sparsification. In addition, FT spectral sparsification can be generalized to FT cut sparsification, for cut-based graph learning. Extensive experiments have confirmed the computational efficiencies and accuracies of the proposed methods for learning on dynamic graphs.

Communication-Optimal Distributed Dynamic Graph Clustering.

We consider the problem of clustering graph nodes over large-scale dynamic graphs, such as citation networks, images and web networks, when graph updates such as node/edge insertions/deletions are observed distributively. We propose communication-efficient algorithms for two well-established communication models namely the message passing and the blackboard models. Given a graph with n nodes that is observed at s remote sites over time [1, t], the two proposed algorithms have communication costs Õ(ns) and Õ(n + s) (Õ hides a polylogarithmic factor), almost matching their lower bounds, Ω(ns) and Ω (n + s), respectively, in the message passing and the blackboard models. More importantly, we prove that at each time point in [1, t] our algorithms generate clustering quality nearly as good as that of centralizing all updates up to that time and then applying a standard centralized clustering algorithm. We conducted extensive experiments on both synthetic and real-life datasets which confirmed the communication efficiency of our approach over baseline algorithms while achieving comparable clustering results.

[Paternally originated Wolf-Hirschhorn syndrome detected by multiplex ligation-dependent probe amplification and microarray comparative genomic hybridization].

OBJECTIVE: To confirm the diagnosis of a Wolf-Hirschhorn syndrome by family study using both cytogenetic and molecular genetic techniques. METHOD: G-band karyotyping was performed for all the 6 members in the family. Multiplex ligation-dependent probe amplification (MLPA) was used to detect the chromosome abnormality for the proband, his father and brother. Microarray comparative genomic hybridization (Array-CGH) was carried out to map the exact chromosomal breakpoints for the proband. RESULT: The proband presented with a typical face, delayed growth and hypotonia in Wolf-Hirschhorn syndrome. His G-band karyotype was 46, XY, der(4)t(4;8) (p16.2; p23.1)pat. MLPA showed 4pter loss and 8pter gain. Array-CGH revealed an XY male with a 3.781 Mb deletion of 4p16.3-p16.2 and a 6.760 Mb duplication of 8p23.3-p23.1. The proband's brother has mental retardation and skeletal abnormalities. His G-band karyotype was 46, XY, der(8)t(4;8)(p16.2;p23.1)pat. MLPA showed 4pter gain and 8pter loss. The proband's father had normal phenotype with a balanced translocation of 46, XY, t(4;8)(p16.2;p23.1)pat. MLPA showed a normal result. The proband's grandfather showed a normal phenotype with a balanced translocation 46, XY, t(4;8)(p16.2;p23.1). The other members in the family showed normal phenotypes with normal karyotypes. CONCLUSION: The proband has features of Wolf-Hirschhorn syndrome with partial monosomy 4p and partial trisomy 8p. The proband's brother has a partial trisomy 4p and partial monosomy 8p. The derived chromosomes are inherited from paternal balanced translocation t(4;8)(p16.2;p23.1).

[Hematologic parameters and genotype analysis in 166 children with HbH disease in the North Guangxi region].

OBJECTIVE: To study the characteristics of genotype spectrum and hematologic parameters in children with HbH disease in the North Guangxi region. METHODS: HbH disease was identified by clinical manifestations, routine blood tests and hemoglobin electrophoresis in 166 children who came form the North Guangxi region. Genotypes were determined by Multi-PCR combined with PCR reverse dot blot. DNA sequencing was used when the genotype could not be identified by regular methods. RESULTS: Of the 166 children with HbH disease, 8 genotypes were identified: --SEA/-α3.7 (82 cases), --SEA/-α4.2 (40 cases), --SEA/αCSα (38 cases), --SEA/αQSα (1 case), --SEA/αWSα (1 case), --SEA/αCD43/44 (-C) α (1 case), --SEA/-α3.7 plus CD17 (A→T) (1 case) and --SEA/-α4.2 plus CD41-42(-TTCT) (1 case). One case was confirmed as the heterozygote of --SEA and an unknown mutation. In the 134 cases with complete medical data, 2 had normal hemoglobin levels, 36 manifested mild anemia, 90 manifested moderate anemia, and 6 (genotype: --SEA/αCSα) showed severe anemia because of the coexistence of infection. Children with the genotype of --SEA/-α3.7 (69 cases), --SEA/-α4.2 (31 cases) and --SEA/αCSα (34 cases) had hemoglobin levels of 62-120, 69-127 and 34-110 g/L respectively. The hemoglobin level in the --SEA/αCSα group was significantly lower than in the deletional HbH disease group (genotypes: --SEA/-α3.7 and --SEA/-α4.2 ) (P<0.05). In contrast, MCV levels in the --SEA/αCSα group were significantly higher than in the deletional HbH disease group (P<0.05). CONCLUSIONS: The genotype spectrum of HbH disease is diverse in the North Guangxi region. Deletional genotype is prevalent. The disease is heterogeneous. The children with --SEA/αCSα HbH disease have severer anemia and higher MCV levels than those with deletional HbH disease.

Detection of alpha-thalassemia in China by using multiplex ligation-dependent probe amplification.

The multiplex ligation-dependent probe amplification (MLPA) method was used to analyze 118 DNA samples from 90 alpha-thalassemia (alpha-thal) patients and 28 normal persons from Southern China, where the main causes of alpha-thal are three large deletions (-alpha3.7, -alpha4.2, and --SEA) and two point mutations in the alpha-globin gene cluster on chromosome 16. The results, detected by the P140B HBA kit, were in complete concordance with the results detected by multiplex polmymerase chain reaction (m-PCR) and real-time PCR. The advantages and limitations of the techniques are discussed. We concluded that MLPA was a rapid and reliable method to determine the cause of both deletional and nondeletional alpha-thal in China.

[A study on the (CA)n in FVIII gene in Han ethnic group in Guangxi Zhuang Autonomous Region by amplification polymorphisms combined with silver staining].

OBJECTIVE: Hemophilia A is an inherited bleeding disorder caused by defects in factor VIII (FVIII) gene. In the present study, the frequencies of the microsatellite alleles at introns 13 and 22 in the factor VIII gene were analyzed in the group of Han nationality in Guangxi Zhuang Autonomous Region to explore their diagnostic value for hemophilia A. These two sites were also used to detect the carriers in 13 hemophilia A families. METHODS: Ninty-one individuals of Han ethnic group in Guangxi Zhuang Autonomous Region (135 X chromosomes) and 13 HA families were subjected to molecular studies. First, these two fragments were PCR amplified simultaneously. Then, silver staining was used later to show their polymorphisms. The investigators selected one sample at random to obtain its lengths of the PCR products at these two sites by ABI310 PCR amplifier. After counting its repeated numbers of (CA) according to the documents concerned, the repeated numbers of the other samples could be counted easily. RESULTS: In the 91 individuals, 6 and 4 alleles were detected at these two sites, respectively. At intron 13 the allele frequencies ranged from 0.0002 to 0.5408 and polymorphism information content (PIC) was 0.5899. At intron 22 the allele frequencies ranged from 0.0444 to 0.4963 and its PIC was 0.5359. The actual heterozygosity for intron 13 and intron 22 were 0.6364 (28/44) and 0.5227 (23/44), respectively. In 13 hemophilia A families with positive history, 9 of them were diagnosed by this method and the diagnosis rate was 69%. CONCLUSION: With high PICs, (CA)n at intron 13 and intron 22 were two valuable sites in the diagnosis of hemophilia A in the population of Han ethnic group in Guangxi Zhuang Autonomous Region. Compared with some other HA restrictive fragment length polymorphisms (RFLP), intron 22 (GT)n (AG)n was more informative.