Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes

Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high resolution. However, few studies have evaluated the performance of different single molecule sequencing platforms for SV detection in human samples. Here we performed Oxford Nanopore Technologies (ONT) whole-genome sequencing of two Swedish human samples (average 32× coverage) and compared the results to previously generated Pacific Biosciences (PacBio) data for the same individuals (average 66× coverage). Our analysis inferred an average of 17k and 23k SVs from the ONT and PacBio data, respectively, with a majority of them overlapping with an available multi-platform SV dataset. When comparing the SV calls in the two Swedish individuals, we find a higher concordance between ONT and PacBio SVs detected in the same individual as compared to SVs detected by the same technology in different individuals. Downsampling of PacBio reads, performed to obtain similar coverage levels for all datasets, resulted in 17k SVs per individual and improved overlap with the ONT SVs. Our results suggest that ONT and PacBio have a similar performance for SV detection in human whole genome sequencing data, and that both technologies are feasible for population-scale studies.

De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

The current human reference sequence (GRCh38) is a foundation for large-scale sequencing projects. However, recent studies have suggested that GRCh38 may be incomplete and give a suboptimal representation of specific population groups. Here, we performed a de novo assembly of two Swedish genomes that revealed over 10 Mb of sequences absent from the human GRCh38 reference in each individual. Around 6 Mb of these novel sequences (NS) are shared with a Chinese personal genome. The NS are highly repetitive, have an elevated GC-content, and are primarily located in centromeric or telomeric regions. Up to 1 Mb of NS can be assigned to chromosome Y, and large segments are also missing from GRCh38 at chromosomes 14, 17, and 21. Inclusion of NS into the GRCh38 reference radically improves the alignment and variant calling from short-read whole-genome sequencing data at several genomic loci. A re-analysis of a Swedish population-scale sequencing project yields > 75,000 putative novel single nucleotide variants (SNVs) and removes > 10,000 false positive SNV calls per individual, some of which are located in protein coding regions. Our results highlight that the GRCh38 reference is not yet complete and demonstrate that personal genome assemblies from local populations can improve the analysis of short-read whole-genome sequencing data.

Changes in alcohol consumption between 2009 and 2014 assessed with the AUDIT

BACKGROUND

Alcohol habits in Sweden, assessed as sales and estimates of unrecorded consumption, have changed since joining the EU. Earlier studies using the Alcohol Use Disorders Identification Test (AUDIT) showed that reported consumption is consistent with sales data, which makes it possible to assess consumption according to sex and age.

AIMS

This study reports the changes in alcohol habits between 2009 and 2014, a period starting a couple of years after Sweden joined the EU.

METHOD

The AUDIT was sent to a random sample of the Swedish population aged between 17 and 80 years old.

RESULTS

No statistically significant changes were shown in six age and sex groups.

CONCLUSIONS

Alcohol habits have stabilised in Sweden but on a higher consumption level than before.

Elderly women above screening age diagnosed with cervical cancer have a worse prognosis

AIM

To analyze the cervical screening history in women with cervical cancer and their outcome.

DESIGN

All women diagnosed with cervical cancer between January 2009 and December 2010 in the South Sweden region were included in the audit.

MATERIALS AND METHODS

Cervical cancer was registered in 165 women in 2009 and 2010. Their screening history was analyzed, and was classified as normal or imperfect. The method of discovering the cancer was either by symptoms or by screening. The main outcome measured was overall survival in cervical cancer related to cervical screening history.

RESULTS

Women above 65 years of age were more frequently diagnosed with advanced-stage disease (The International Federation of Gynecology and Obstetrics II-IV) (n=36 out of 43; 84%) compared to women below 65 years of age (n=35 out of 122; 29%) (p<0.001). All patients diagnosed by the cervical screening program were still alive (30/30) at the median follow-up time (36 months), showing better overall survival compared to women below screening age in whom cancer was discovered due to symptoms (68/98; p<0.001). Cox proportional hazards model showed that women beyond screening age (>65 years old) with normal screening history had a worse prognosis, with a hazard ratio of 4.8 (95% confidence interval=1.9-12.1, p=0.001), and women (>65 years old) who had not followed the screening program had a hazard ratio of 5.9 (95% confidence interval I 2.4-14.6, p<0.001), compared to women under 65 years old who had followed the screening program.

CONCLUSION

Cervical cancer in women above the age of 65 years is discovered at advanced stages of the disease and their prognosis is poor.

Family history interview of a broad phenotype in specific language impairment and matched controls

The aim was to study a broader phenotype of language-related diagnoses and problems in three generations of relatives of children with specific language impairment (SLI). Our study is based on a family history interview of the parents of 59 children with SLI and of 100 matched control children, exploring the prevalence of problems related to language, reading, attention, school achievement and social communication as well as diagnoses such as attention-deficit hyperactivity disorder (ADHD), autism, Asperger syndrome, dyslexia, mental retardation, cleft palate and stuttering. The results show a spectrum of language-related problems in families of SLI children. In all three generations of SLI relatives, we found significantly higher prevalence rates of language, literacy and social communication problems. The risk of one or both parents having language-related diagnoses or problems was approximately six times higher for the children with SLI (85%) than for the control children (13%) (odds ratio = 37.2). We did not find a significantly higher prevalence of the diagnoses ADHD, autism or Asperger syndrome in the relatives of the children with SLI. However, significantly more parents of the children with SLI had problems with attention/hyperactivity when compared with the parents of controls. Our findings suggest common underlying mechanisms for problems with language, literacy and social communication, and possibly also for attention/hyperactivity symptoms.