The advantages of both the length and accuracy of high-fidelity (HiFi) reads enable chromosome-scale haplotype-resolved genome assembly. In this study, we sequenced a cell line named HJ, established from a Chinese Han male individual by using HiFi and Hi-C. We assembled two high-quality haplotypes of the HJ genome (haplotype 1 (H1): 3.1 Gb, haplotype 2 (H2): 2.9 Gb). The continuity (H1: contig N50 = 28.2 Mb, H2: contig N50 = 25.9 Mb) and completeness (BUSCO: H1 = 94.9%, H2 = 93.5%) are substantially better than those of other Chinese genomes, for example, HX1, NH1.0, and YH2.0. By comparing HJ genome with GRCh38, we reported the mutation landscape of HJ and found that 176 and 213 N-gaps were filled in H1 and H2, respectively. In addition, we detected 12.9 Mb and 13.4 Mb novel sequences containing 246 and 135 protein-coding genes in H1 and H2, respectively. Our results demonstrate the advantages of HiFi reads in haplotype-resolved genome assembly and provide two high-quality haplotypes of a potential Chinese genome as a reference for the Chinese Han population.

BACKGROUND: Although gender differences in major depressive disorder (MDD) have been widely reported, there has not been much focus on gender differences in comorbidity. In patients with MDD and comorbid metabolic syndrome (Mets), the goal of this study was to investigate potential gender differences in the prevalence and clinical correlates of concomitant anxiety.
METHODS: Seven hundred and ninety-four first-episode and drug-naïve patients (FEDN) patients with MDD and comorbid Mets were recruited. For each patient, sociodemographic data, thyroid function indicators, and Mets parameters were acquired. Each participant completed the 14-item Hamilton Assessment Scale for Anxiety (HAMA) and the 17-item Hamilton Assessment Scale for Depression (HAMD).
RESULTS: There were no gender differences in the prevalence of anxiety in patients with MDD and comorbid Mets. Female patients with MDD had a shorter duration of illness. Correlation analysis showed that HAMD score, TSH, TgAb, and TPOAb were associated with anxiety prevalence in female patients, whereas anxiety onset in male patients was only associated with TSH, TgAb, and TPOAb levels. In addition, multiple logistic regression analysis showed that TSH and TgAb predicted anxiety in male patients, whereas HAMD score and age of onset significantly predicted anxiety in female patients.
CONCLUSIONS: Cross-sectional design and no control for anxiety-related factors.
CONCLUSIONS: Our study showed no gender differences in the prevalence of anxiety in patients with MDD and comorbid Mets. HAMD score was associated with anxiety in female patients, whereas TSH, TgAb, and TPOAb were associated with anxiety in male patients.

People with schizophrenia are more likely to be afflicted by obesity or overweight compared to the general population. This study aimed to explore the incidence of overweight and obesity, clinical features and cognitive performance of Chinese Han patients with chronic schizophrenia who had overweight or obesity. We obtained data from 985 schizophrenia inpatients about overweight and obesity through body mass index (BMI). All patients were evaluated with the positive and negative syndrome scale, the Mini-mental State Examination (MMSE) and the repeated battery for evaluation of the neuropsychological status (RBANS) scale. We collected demographic and clinical data using self-reported questionnaires. We divided patients into normal weight (BMI < 24 kg/m2), overweight (24 ≤ BMI < 28 kg/m2) and obese (≥28 kg/m2) groups according to the Working Group on Obesity in China (WGOC) criteria. We compared the clinical data between the three groups and then conducted binary logistic regression and linear regression to assess variables that were significantly associated with overweight and obesity and higher BMI. Of the sample, 324 (32.9%) and 191 (19.4%) patients had overweight and obesity, respectively. Patients who had overweight and obesity were younger, had less education, had higher waist and hip circumferences, higher rates of diabetes and a higher sumPANSP score (compared with patients in the normal group, p < 0.05). There were more female patients with obesity (compared with patients in the normal and overweight groups, p < 0.05). Logistic regression analysis indicated that overweight and obesity were associated with sumPANSP (OR = 1.03, 95%CI = 1-1.061, p = 0.049) and diabetes (OR = 1.891, 95%CI = 1.255-2.849, p = 0.002). Further linear regression showed that age (B = -0.004, t = -2.83, p = 0.005), educational level (B = -0.037, t = -2.261, p = 0.024), diabetes (B = 0.133, t = 2.721, p = 0.007) and sumPANSP (B = 0.008, t = 2.552, p = 0.011) were risk factors for higher BMI. We did not find cognitive performance differences between patients with or without overweight and obesity. Overweight and obesity were associated with some demographic and clinical factors in patients with persistent schizophrenia.

OBJECTIVE: The objective of the study was to clarify the associations of HLA class I and II alleles with ankylosing spondylitis (AS) among Chinese Han.
METHODS: We performed HLA genotyping and Sanger sequencing for 68 HLA-B*27(-), 62 HLA-B*27(+) AS patients, and 70 controls. Case-control analyses and separate analyses of HLA-B*27(-) patients were performed. One-way ANOVA and Kruskal-Wallis multiple comparisons test were used to analyze the effects of HLA-A\\B\\C\\DRB1\\DQB1 alleles on clinical characteristics of HLA-B*27(-) and HLA-B*27(+) patients.
RESULTS: In the HLA-B*27(+) group, positive associations were seen with A*11:02, B*27:04, B*27:05, C*02:02, C*12:02, and DRB1*04:01 and negative associations were seen with A*33:03, B*07:02, B*57:01, and C*07:02. The age at onset was greater in HLA-B*27(-) patients than in HLA-B*27(+) patients (30.03 ± 15.15 vs. 23.08 ± 7.79 years). In the HLA-B*27(-) group, those with A*01:01, B*13:01, B*13:02, C*01:02, C*04:01, DQB1*02:01, DQB1*06:01, and DRB1*03:01 had an earlier onset than those without these alleles, while patients carrying B*40:02, C*07:02, C*12:02, C*15:02, DQB1*05:02, and DQB1*05:03 had a delayed onset. In the HLA-B*27(-) group, A*32:01(+), C*08:01(+), and DRB1*04:05(-) women were likely to develop AS. In the HLA-B*27(+) group, DQB1*03:02(+) women may be more likely to develop AS. DRB1*12:02 and HLA-B*27 interacted with the distribution of AS-affected sites. In the HLA-B*27(+) group, DRB1*12:02(+) patients were likely to have peripheral joint involvement.
CONCLUSIONS: HLA class I and II alleles other than HLA-B*27 contribute to AS predisposition and characteristics among Chinese Han patients.

Genetic polymorphism of the cytochrome P450 (CYP) gene can significantly influence the metabolism of endogenous and xenobiotic compounds. However, few studies have focused on the polymorphism of CYP2J2 and its impact on drug catalytic activity, especially in the Chinese Han population. In this study, we sequenced the promoter and exon regions of CYP2J2 in 1,163 unrelated healthy Chinese Han individuals using the multiplex PCR amplicon sequencing method. Then, the catalytic activities of the detected CYP2J2 variants were evaluated after recombinant expression in S. cerevisiae microsomes. As a result, CYP2J2*7, CYP2J2*8, 13 variations in the promoter region and 15 CYP2J2 nonsynonymous variants were detected, of which V15A, G24R, V68A, L166F and A391T were novel missense variations. Immunoblotting results showed that 11 of 15 CYP2J2 variants exhibited lower protein expression than wild-type CYP2J2.1. In vitro functional analysis results revealed that the amino acid changes of 14 variants could significantly influence the drug metabolic activity of CYP2J2 toward ebastine or terfenadine. Specifically, 4 variants with relatively higher allele frequencies, CYP2J2.8, 173_173del, K267fs and R446W, exhibited extremely low protein expression and defective catalytic activities for both substrates. Our results indicated that a high genetic polymorphism of CYP2J2 could be detected in the Chinese Han population, and most genetic variations in CYP2J2 could influence the expression and catalytic activity of CYP2J2. Our data significantly enrich the knowledge of genetic polymorphisms in CYP2J2 and provide new theoretical information for corresponding individualized medication in Chinese and other Asian populations.

Overweight/obese major depressive disorder (MDD) patients have a high probability of developing glucose metabolism disorders; however, the results are inconsistent due to the confounding variables involved in the studies. The purpose of this study was to explore the prevalence and risk factors for elevated fasting glucose in Chinese Han patients with overweight/obese first-episode and drug naïve (FEDN) MDD.
The study used a cross-sectional design and recruited 1718 FEDN MDD patients between the ages of 18 and 60 years. Socio-demographic information, anthropometric data, and biochemical parameters were collected. The 17-item Hamilton Assessment Scale for Depression (HAMD), the 14-item Hamilton Anxiety Scale (HAMA), and the Positive and Negative Syndrome Scale (PANSS) positive subscale were used to assess symptoms of all patients.
MDD patients with elevated fasting glucose had higher TSH, TPOAb, TC, TG, LDL-C, systolic and diastolic blood pressure levels than those with normal fasting glucose. Logistic regression analysis showed that age, TSH, TgAb, TPOA, and TG were related factors for elevated fasting glucose, while TSH and combination all these five parameters had the potential to differentiate between patients with elevated fasting glucose and those with normal fasting glucose. Multifactorial regression analysis showed that TSH, TG, and LDL-C were independently associated with elevated fasting glucose.
Our findings suggest a high prevalence of elevated fasting glucose in overweight/obese FEDN MDD patients. Several clinically relevant factors and metabolic parameters are associated with elevated fasting glucose in overweight/obese FEDN MDD patients.
Due to the cross-sectional design, no causal relationship could be derived.

Juvenile idiopathic arthritis (JIA) refers to a group of chronic childhood arthropathies of unknown etiology. In the present study, the genetic association between the variants in PTPN22, IRF5 and TYK2 genes and susceptibility to JIA was investigated. The distributions of 16 variants in PTPN22, IRF5 and TYK2 genes were analyzed by direct sequencing in 378 patients with JIA and 378 healthy controls. Odds ratios and 95% confidence intervals were used to evaluate the association between the gene variants and JIA. The gene-gene interactions were investigated using multifactor dimensionality reduction. All allelic and dominant models of PTPN22 rs1214414, rs1214418, rs1746853, rs3765598 and rs3811021 were significantly associated with JIA risk (P<0.05). IRF5 rs10954213 in both allelic and dominant models, as well as the allelic model of rs2004640, was significantly related to JIA risk (P<0.05). In addition, the allelic, recessive and dominant models of TYK2 rs280500, rs280519, rs2304256 and rs12720270 were significantly related to JIA risk (P<0.05). In addition, three haplotypes (HC A G T C C, HC A G T T C and HC G T T C T ) in PTPN22 gene, three haplotypes (HD T A A, HI T A C and HD T G C) in IRF5 gene and two haplotypes (HA G G A T and HG A G G T) in TYK2 gene were associated with the risk of JIA (P<0.05). Furthermore, a three-way interaction between IRF5 rs10954213, rs2004640 and PTPN22 rs1214414 was shown to be associated with JIA risk. In conclusion, PTPN22 rs1214418, rs1746853, rs3765598, IRF5 rs2004640, TYK2 rs280500, rs2304256 and a three-way interaction between IRF5 rs10954213, rs2004640 and PTPN22 rs1214414 may be risk factors for JIA.

X-chromosomal markers have been proved as a useful tool for solving complex kinship cases due to its sex-linked inheriting feature. Among these markers, tightly linked X-STR clusters forming haplotypes are highly informative. The analysis of the haplotypes requires determination of linkage disequilibrium. In this study, genetic linkage, recombination fractions and mutation rates of 38 X-STR loci in 177 three-generation pedigrees were investigated. Genetic linkage analysis and calculation of recombination fractions were performed within each pair of markers and clusters. Then mutation rates were calculated. The results showed that, a) 22 recombination events happened within the tightly linked X-STR clusters, which span<1.0 Mb; b) significantly linked marker pairs were observed with the LOD (logarithm of the odds) scores > 2.0 (2.0104 to 54.8316); c) the average mutation rate of the 38 X-STR loci was 1.32 × 10-3 per meiosis in the Chinese Han population, with DXS10135 and DXS8377 presenting notably high mutation rate (6.5 × 10-3). Our results confirmed that meiotic recombination was not a simple function of physical distance, so that whether recombination occurred at the closely clustered X-STRs or not should be assumed cautiously considering the stability of haplotypes in inheritance process for kinship analysis. This study supplemented the existing database and laid an experimental foundation for the future study on genetic characteristics, recombination, and mutation of the X-STRs.

The disparities of hr-HPV infection among races/ethnicities have not been fully discussed. This study aimed to investigate the difference of hr-HPV infection between Chinese Han and Mongols minority women in Inner Mongolia.
Genotyping and histopathology data of Chinese Han and Mongols minority women in Inner Mongolia from Chinese Multi-Center Screening Trial were used to analyze the hr-HPV prevalence, and type-specific distribution in abnormal pathology results.
The hr-HPV infection rates of Han women was 15.9% while of Mongols was 21.6% (P < 0.001). The most prevalent genotypes in Han women were ranked as HPV-16,-52,-18/-58,-31/-39, and-59 while in Mongols were-16,-31,-58,-18 and-52. When analyzing the age-specific of hr-HPV infection, two peaks were found at age of 40-44 (20.5%) and 55-59 (23.5%) years in Han women while three peaks were observed at age of 30-34 (22.1%), 45-49 (22.9%), and 55-59 (31.8%) years, respectively, in Mongols. HPV-16 accounting for 62.5 and 53.8% of the CINII+ in Han and Mongols, respectively.
The prevalence of hr-HPV was significantly different between the Han and Mongols minority women in Inner Mongolia, races/ethnicities background should be taken into consideration for the refinement of cervical cancer screening strategies and vaccine implementation in China.

Aims: The toll-like receptor (TLR) genes were shown to be involved in the pathogenesis of rheumatoid arthritis (RA). We aimed to investigate the genetic associations between the TLR-1, -2, -4, and -6 genes polymorphisms with RA susceptibility in a Chinese Han population. Methods: Six polymorphisms [TLR-1 (rs5743610, rs5743618), -2 (rs5743708), -4 (rs4986790, rs4986791), and -6 (rs5743810)] in TLRs genes were genotyped in 360 patients with RA and 560 matched healthy controls by direct sequencing. The odds ratios (ORs) and 95% confidence intervals (CIs) were evaluated using a standard logistic regression analysis. Results: No significant associations were observed under the allelic, dominant, or recessive models for TLR-1 rs5743610, TLR-2 rs5743708, TLR-4 rs4986790 and rs4986791, and TLR-6 rs5743810 polymorphisms and RA risk (all p > 0.05). However, significant associations were detected under the allelic, dominant, and recessive models for TLR-1 rs5743618 and RA risk (allelic: OR [95% CI] = 2.21 [1.73-2.81], p < 0.0001; dominant: OR [95% CI] = 2.33 [1.75-3.09], p < 0.0001; recessive models: OR [95% CI] = 3.70 [1.85-7.41], p = 0.0002). In addition, TLR6 rs5743810 was found to be associated with the rheumatoid factor (RF)- and anticyclic citrullinated peptide (anti-CCP)- antibody in RA group (RF: OR [95% CI] = 2.29 [1.42-3.69], p = 0.0007; anti-CCP: OR [95% CI] = 2.33 [1.39-3.89], p = 0.001). Conclusions: The allelic, dominant, and recessive models of TLR1 rs5743618 might be associated with RA susceptibility. Also, the TLR6 rs5743810 marker may be associated with RF and the anti-CCP antibody of RA in the Chinese Han population.