Annotating cell types is a critical step in single-cell RNA sequencing (scRNA-seq) data analysis.Some supervised or semi-supervised classification methods have recently emerged to enable automated cell type identification.However,comprehensive evaluations of these methods are lacking.Moreover,it is not clear whether some classification methods originally designed for ana-lyzing other bulk omics data are adaptable to scRNA-seq analysis.In this study,we evaluated ten cell type annotation methods publicly available as R packages.Eight of them are popular methods developed specifically for single-cell research,including Seurat,scmap,SingleR,CHETAH,Sin-gleCellNet,scID,Garnett,and SCINA.The other two methods were repurposed from deconvolut-ing DNA methylation data,i.e.,linear constrained projection (CP) and robust partial correlations(RPC).We conducted systematic comparisons on a wide variety of public scRNA-seq datasets as well as simulation data.We assessed the accuracy through intra-dataset and inter-dataset predic-tions;the robustness over practical challenges such as gene filtering,high similarity among cell types,and increased cell type classes;as well as the detection of rare and unknown cell types.Over-all,methods such as Seurat,SingleR,CP,RPC,and SingleCellNet performed well,with Seurat being the best at annotating major cell types.Additionally,Seurat,SingleR,CP,and RPC were more robust against downsampling.However,Seurat did have a major drawback at predicting rare cell populations,and it was suboptimal at differentiating cell types highly similar to each other,compared to SingleR and RPC.All the code and data are available from https://github.com/qian-huiSenn/scRNA_ cell_ deconv_benchmark.

Objective To study the correlation between polymorphism of intron 5 gene of surfactant protein B(SP-B)and bronchopulmonary dysplasia(BPD) in neonates and to explore the relevance of the pathogenesis of BPD at the genetic level.Methods Fifty infants with BPD admitted to the NICU in the Hos-pital of Inner Mongolia Medical University from November 2016 to November 2017 were selected as the BPD group.Among them,13 were Mongolian nationality,37 were Han nationality. Fifty newborn without BPD during the same period were assigned to the control group in this study,among them,15 were Mongolian na-tionality,35 were Han nationality.PCR technique was used to detect SP-B gene intron 5 polymorphism and its genotype and allele distribution. Results Regardless of Mongolian or Han nationality,three genotypes of SP-B intron 5 genotypes were detected:wild type,insert type and deletion type.The frequencies of the three genotypes were 73.0%(27/37),10.8%(4/37) and 16.2%(6/37) respectively,and the allele frequencies were 77.0%(57/74),9.5%(7/74) and 13.5%(10/74) respectively in the Han nationality BPD group.The frequencies of the three genotypes in the Han nationality control group were 82.9%(29/35),11.4%(4/35) and 5.7%(2/35)respectively;the allele frequencies were 85.7%(60/70),8.6%(6/70) and 5.7%(4/70) respectively.In the Mongolian BPD group,the frequencies of the above three genotypes were 53.8%(7/13), 15.4%(2/13) and 30.8%(4/13) respectively,and the allele frequencies were 61.5%(16/26),15.4%(4/26) and 23.1%(6/26) respectively.The frequencies of the above three genotypes in the Mongolian con-trol group were 53.3%(8/15),26.7%(4/15) and 20.0%(3/15),the allele frequencies were 66.7%(20/30),20.0%(6/30),13.3%(4/30) respectively.There were no significant differences in the allele fre-quencies and the genotypes of SP-B intron 5 between the Han nationality BPD group and the Han control group,the Mongolian BPD group and the Mongolian control group(all P>0.05).Conclusion No poly-morphisms of SP-B intron 5 and BPD in newborns of the Han nationality and Mongolian nationnality in Inner Mongolia are found.

Objective To study the polymorphism of vascular endothelial growth factor ( VEGF) gene－460T ＞C locus and its correlation with bronchopulmonary dysplasia ( BPD ) in preterm infants. Method From October 2014 to October 2017, a prospective study was conducted on BPD preterm infants admitted to the neonatal department of the Affiliated Hospital of Inner Mongolia Medical University .During the same time, non-BPD preterm infants of the same nation and same ethnic group were selected as the control group.The ratio between the BPD group and the control group was 1∶1.Genotype and allelic distribution of VEGF－460T＞C loci in both groups were detected using polymerase chain reaction method . Result A total of 100 BPD infants were enrolled in the BPD group , including 50 cases of Mongolian nationality and 50 cases of Han nationality.Both TT and CT genotypes were detected in the VEGF －460T＞C locus in the BPD and control groups .The frequencies of the two genotypes were 38.0%and 62.0%in the BPD group, 29.0% and 71.0% in the control group.The C allele frequencies were 31.0% in the BPD group and 35.5%in the control group.The T allele frequencies were 69.0%in the BPD group and 64.5%in the control group.No significant differences existed in allele and genotype frequencies between the two groups (P＝0.178 and 0.338).The frequencies of the two genotypes in the Mongolian BPD infants and the Han BPD infants were 40.0%and 60.0%vs.36.0%and 64.0%.The C allele frequencies were 30.0%and 32.0%, and the T allele frequencies were 70.0% and 68.0%.No significant differences existed in allele and genotype frequencies between the two groups ( P ＝0.680 and 0.648 ) .Conclusion No correlation existed between the polymorphism of VEGF －460T＞C locus and the occurrence and development of BPD in premature infants in Inner Mongolia.

Objective:To explore the relationship between rs2010963, rs3025039 and rs699947 gene polymorphism of vascular endothelial growth factor(VEGF) gene and bronchopulmonary dysplasia(BPD) in Mongolian premature infants.Methods:A case-control design was used to collect 50 cases of Mongolian premature infants who were hospitalized at the Affiliated Hospital of Inner Mongolia Medical University and diagnosed with BPD from January 2016 to December 2020 as the observation group, while 56 cases of non-BPD premature infants of the same nationality and time period were selected as the control group.Using PCR method to detect the genotype and allele distribution of the VEGF gene rs2010963, rs3025039 and rs699947 locus.Combining clinical data to analyze whether the above gene loci were related to the onset of premature infants with Mongolian BPD in our area.Results:Through genetic testing, it was found that CC, CA and AA genotypes can be detected at the rs699947 site of VEGF gene in premature infants in both the observation group and the control group.The frequencies of the three genotypes in the observation group were 16.0%, 24.0%, and 60.0%, respectively; the frequency of the C allele was 28.0%, the frequency of the A allele was 72.0%, and the frequency of the three genotypes in the control group was 32.1.%, 32.1% and 35.7%, respectively.The frequency of C allele was 48.2%, the frequency of G allele was 51.8%, and the allele and genotype frequencies of this locus between the observation group and the control group were significant differences from those of the control group( P<0.05). Conclusion:The polymorphism of VEGF gene rs699947 locus is associated with the occurrence and development of BPD in Mongolian premature infants, and allele A may be a susceptible factor.

Objective To study the relationship between exon10 region mutation of adenosine triphosphate-binding cassette transporters A3 (ABCA3) gene and neonatal respiratory distress syndrome (RDS).Method From September 2014 to January 2018,neonates admitted to the neonatal intensive care unit of our hospital were studied.Mongolian and Han Chinese newborns with RDS were assigned into Mongolian RDS group and Han RDS group.Mongolian and Han Chinese newborns without RDS were assigned into Mongolian control group and Han control group.The genotype frequencies and allele frequencies of ABCA3 exon10 in each group were compared.Result A total of 320 cases were studied,including 60 cases in Mongolian RDS group,100 cases in Han RDS group,60 cases in Mongolian control group,and 100 cases in Han control group.A single-base point mutation C ＞ T in the ABCA3 rs13332514 (F353F) locus was founded in both Mongolian and Han Chinese newborns.The mutation rates in Mongolian RDS group and Mongolian control group were 26.7％ and 18.3％,and the difference was statistically significant (x2 =6.316,P =0.043);the mutation rates in Han RDS group and Han control group were 21.0％ and 13.0％,the difference was also statistically significant (x2 =7.426,P =0.009).No significant differences existed between Mongolian RDS group and Han RDS group,and between Mongolian control group and Han control group (P ＞ 0.05).The genotypes of CC,CT and TT were detected in both Mongolian and Han RDS groups,and the CC and CT genotypes were also detected in the control group.The T allele frequency was 18.3％ in Mongolian RDS group,and 9.2％ in Mongolian control group.The difference was statistically significant (x2 =4.251,P =0.039).The T allele frequency in Han RDS group was 15.0％,and 6.5％ in Han control group.The difference was also statistically significant (x2 =7.530,P =0.006).Conclusion A single-base point mutation C ＞T in the rs13332514 (F353F) locus of ABCA3 exonl0 may be related to the occurrence of RDS in Mongolian and Han newborns in Inner Mongolia.Allele T may be one of the susceptibility genes of RDS.

Objective:To explore the carrier status of group B streptococci (GBS) in pregnant women of Mongolian and Han nationality and the neonatal GBS infection in order to identify the high risk factors of GBS infection in Mongolian and Han newborns in this area.Methods:Totally 7289 pregnant women and their newborns born alive were tested for GBS in the Affiliated Hospital of Inner Mongolia Medical University from June 2017 to June 2020, and their newborns were cultured for GBS, and the venous blood of newborns delivered by GBS positive women were detected for anti-GBS capsular polysaccharide antibody level, in order to determine the high risk factors of neonatal GBS infection.Results:Among the 7289 pregnant women, 3136 were Mongolian pregnant women (2599 full-term delivery and 537 premature delivery) and 4153 were Han pregnant women (3541 full-term delivery and 612 premature delivery). The results of GBS test showed that the GBS carrier rate was 8.19% in the Mongolian preterm delivery group, 4.35% in the Mongolian term group, 11.93% in the Han preterm group, and 5.76% in the Han term group, indicating that the carrier rate of GBS in the preterm group was significantly higher than that in the term group, regardless of Mongolian and Han nationality ( P < 0.05). Further comparing the GBS carrier rate of Mongolian and Han pregnant women, the GBS carrier rate of Mongolian pregnant women was significantly lower than that of Han pregnant women regardless of the premature delivery group and term group ( P < 0.05). (2) A total of 434 newborns were born by GBS positive parturients. The positive rates of GBS in Mongolian premature infants, Mongolian full-term infants, Han premature infants and Han full-term infants were 29.55%, 14.16%, 31.51% and 17.65%, respectively, suggesting that the positive rate of GBS in premature infants was significantly higher than that in full-term infants, regardless of Mongolian and Han nationality ( P<0.05). Further comparing the positive rate of GBS in Mongolian and Han newborns, there was no significant difference in the positive rate of GBS between Mongolian newborns and Han newborns, no matter the premature delivery group and the full-term group. (3) This study compared the incidence of early-onset GBS septicemia in Mongolian and Han newborns. The results showed that the incidence of early-onset GBS septicemia in Mongolian premature infants was 23.08%, and none in full-term infants. The incidence of early-onset GBS septicemia in Han premature infants was 26.09%. The incidence of early-onset GBS septicemia in term infants was 5.56%. The incidence of neonatal GBS septicemia in the preterm group was significantly higher than that in the term group, regardless of Mongolian and Han nationality. By further comparing the incidence of GBS septicemia in Mongolian and Han newborns, there was no significant difference in the positive rate of GBS between Mongolian newborns and Han newborns regardless of the premature delivery group and the term group. (4) In both Mongolian and Han nationality, the level of anti-GBS capsular polysaccharide antibody in premature infants was significantly lower than that in term infants ( P < 0.05). (5) Regardless of the Mongolian and Han nationality, compared with GBS negative group, GBS positive rate was higher in pregnant women aged≥35 years old, with history of menstruation, miscarriage, vaginitis, floating population, and those who had not undergone pre-pregnancy examination,,which were the high risk factors for GBS-positive pregnant women during pregnancy. (6) In both Mongolian and Han nationality, the incidence of chorioamnionitis, puerperal infection, premature delivery and premature rupture of membranes in the GBS positive group was higher than that in the GBS negative group, and the incidence of fetal distress and neonatal asphyxia in the GBS positive group was also higher than that in the GBS negative group. Conclusions:The carrier rate of GBS in Mongolian pregnant women is lower than that in Han pregnant women, and positive GBS during pregnancy will increase the incidence of adverse maternal and fetal outcomes such as chorioamnionitis, puerperal infection, premature delivery, premature rupture of membranes, fetal distress, neonatal asphyxia and neonatal early-onset GBS septicemia. The high risk factors are maternal age ≥ 35 years old, history of menstruation, abortion, vaginitis, floating population, and infection without pre-pregnancy examination. We should attach great importance to the perinatal high risk factors and formulate corresponding intervention measures accordingly, and make rational use of antibiotics for prenatal prevention, so as to further reduce the incidence of early-onset GBS septicemia in newborns.