Towards a reference genome that captures global genetic diversity

The current human reference genome is predominantly derived from a single individual and it does not adequately reflect human genetic diversity. Here, we analyze 338 high-quality human assemblies of genetically divergent human populations to identify missing sequences in the human reference genome with breakpoint resolution. We identify 127,727 recurrent non-reference unique insertions spanning 18,048,877 bp, some of which disrupt exons and known regulatory elements. To improve genome annotations, we linearly integrate these sequences into the chromosomal assemblies and construct a Human Diversity Reference. Leveraging this reference, an average of 402,573 previously unmapped reads can be recovered for a given genome sequenced to ~40X coverage. Transcriptomic diversity among these non-reference sequences can also be directly assessed. We successfully map tens of thousands of previously discarded RNA-Seq reads to this reference and identify transcription evidence in 4781 gene loci, underlining the importance of these non-reference sequences in functional genomics. Our extensive datasets are important advances toward a comprehensive reference representation of global human genetic diversity.

The human reference genome does not fully reflect human genetic diversity. Here, the authors analyse 338 human genome assemblies from diverse populations to identify missing sequences, define non-reference unique insertions and construct a Human Diversity Reference.

Association of arterial stiffness in non-hypertensive offspring with parental hypertension: the Hanzhong adolescent hypertension cohort study

OBJECTIVE

Arterial stiffness may be an early marker for vascular changes associated with hypertension in young adults. Individuals with a family history of hypertension are at high risk of developing hypertension. We investigated whether arterial stiffness measured, such as mean arterial pressure (MAP) and brachial to ankle pulse wave velocity (baPWV), were increased in normotensive offspring with a parental history of hypertension.

PATIENTS AND METHODS

We compared MAP and baPWV in a sample of 1953 non-hypertensive participants (974 men, mean age 42±3 years) recruited in the previous Hanzhong adolescent hypertension cohort study. Standardized questionnaires, physical examinations and laboratory tests were used to obtain information, with a particular focus on family hypertension history, anthropometric, hemodynamic, and biochemical factors.

RESULTS

A total of 1039, 759, 155 participants had 0, 1, and 2 parents with hypertension, respectively. Parental hypertension was associated with elevated offspring MAP (in multivariable-adjusted models, B=1.5 mm Hg, 95% CI 0.8-2.2 for 1 parent with hypertension; B=3.0 mm Hg, 95% CI 1.8-4.3, for 2 parents with hypertension; p<0.001 for each). A significant positive correlation was also observed between MAP and baPWV (r=0.543, p<0.001). BaPWV displayed a similar correlation with parental hypertension in age-adjusted, sex-adjusted and body mass index (BMI)-adjusted models (B=23.1 cm/s, 95% CI 8.0-38.1, for 1 parent with hypertension, p<0.01; B=53.0 cm/s, 95% CI 25.8-80.2, p<0.001 for 2 parents with hypertension), but associations were attenuated in multicovariate models after adjustment for MAP. In multivariable-adjusted models, logistic regression analysis showed that the risk of belonging to the upper quartile of MAP was significantly increased for offspring whose parents had hypertension (OR=1.5, 95% CI 1.2-1.9, for 1 parent with hypertension; OR=2.3, 95% CI 1.6-3.4, for 2 parents with hypertension; p<0.001 for each). Similarly, the odds ratios of belonging to the upper quartile of baPWV increased (OR=1.3, 95% CI 1.1-1.6, for 1 parent with hypertension, p<0.05; OR=2.1, 95% CI 1.5-3.0, for 2 parents with hypertension, p<0.001, in age-sex-BMI-adjusted models), and were then brought down in the fully adjusted models including MAP, but the increase remained significant for 2 parents with hypertension (OR=1.6, 95% CI 1.0-2.3, p<0.05).

CONCLUSIONS

These findings provide evidence that arterial stiffness is higher in young-to middle-aged normotensive subjects with a family history of hypertension, suggesting that increased arterial stiffness may occur in the early stages during the pathogenesis of hypertension.

Evaluation of cell transplant-mediated attenuation of diffuse injury in experimental autoimmune encephalomyelitis using onVDMP CEST MRI

The development and translation of cell therapies have been hindered by an inability to predict and evaluate their efficacy after transplantation. Using an experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis (MS), we studied attenuation of the diffuse injury characteristic of EAE and MS by transplanted glial-restricted precursor cells (GRPs). We assessed the potential of on-resonance variable delay multiple pulse (onVDMP) chemical exchange saturation transfer (CEST) MRI to visualize this attenuation. Allogeneic GRPs transplanted in the motor cortex or lateral ventricles attenuated paralysis in EAE mice and attenuated differences compared to naïve mice in onVDMP CEST signal 5 days after transplantation near the transplantation site. Histological analysis revealed that transplanted GRPs co-localized with attenuated astrogliosis. Hence, diffuse injury-sensitive onVDMP CEST MRI may complement conventional MRI to locate and monitor tissue regions responsive to GRP therapy.

[The correlation between blood pressure response to cold pressor test and long-term blood pressure changes]

Objective: The aim of the study was to investigate the correlation between blood pressure response to cold pressor test (CPT) and follow-up blood pressure after 8 years in subjects, and to evaluate the predictive value of CPT for long-term blood pressure levels. Methods: A total of 365 individuals from eight natural villages were enrolled by stratified cluster sampling from Mei County, Shaanxi Province in 2004. Baseline characteristics of subjects were collected and CPTs were conducted. Subjects were followed up in 2009 and 2012, respectively. According to the maximal change of systolic response (SR), the area under the curve (AUC) of systolic blood pressure change (AUC-SBP), the maximal change of diastolic response (DR) and the AUC of diastolic blood pressure change (AUC-DBP) in CPT, the individuals were divided into four quartile groups by above parameters, respectively: group Ⅰ (P(25)), group Ⅱ (P(50)), group Ⅲ (P(75)) and group Ⅳ (P(100)). The correlation between blood pressure response to CPT and the follow-up blood pressure was analyzed. Results: (1) There were no significant differences in baseline blood pressure levels and prevalence of hypertension among four quartile groups no matter it was grouped on SR, DR, AUC-SBP or AUC-DBP. (2) The prevalence of hypertension in each group from lowest (P(25)) to highest (P(100)) in 2012 was 25.64%, 30.67%, 38.03%, 55.74% on SR grouping (P<0.01), and 27.5%, 29.17%, 38.46%, 57.35% on AUC-SBP grouping (P<0.05), respectively. (3) There were no significant differences in the prevalence of hypertension among four groups in 2012 (P>0.05) either on DR or on AUC-DBP grouping. (4) The random effects model analysis showed that the correlation coefficient between SR, AUC-SBP and long-term systolic blood pressure increase were 1.91 (P<0.05) and 1.44 (P<0.05), respectively, and the correlation coefficient between DR, AUC-DBP and long-term diastolic blood pressure increase were 0.82 (P<0.05) and 0.78 (P>0.05), respectively. Age, male, body mass index, and fasting blood glucose were independent risk factors for long-term blood pressure elevation, and age, body mass index and fasting blood glucose positively correlated with changes in long-term blood pressure (all P<0.05). Conclusion: Individual systolic blood pressure response to CPT can be used as a predictor of long-term hypertension.

44 Wirral's Teletriage Service

Introduction

The Wirral Teletriage Service provides non-urgent clinical support to Wirral Care Homes in order to help avoid unnecessary hospital admissions for their residents. It also aims to provide quicker access to clinical assessment than via NHS 111 and to provide this care in the patient’s residence wherever possible.

Methods

Care homes call the Teletriage service when they have concerns about the health of one of their residents. The Teletriage nurse undertakes a clinical assessment of the resident remotely via Skype. Care Homes have been provided with a secure NHS email address to facilitate secure sharing of data. They have also been provided with iPads and training for their staff. After being assessed by Teletriage, residents are signposted to the most appropriate care pathway for their needs.

Results

76 Care Homes have signed up to the service. On average, the Teletriage Service receives 300-400 calls a month. In an 18 month period, the number of calls to NHS 111 have reduced by 76%. Out of all the calls to Teletriage, 22% of patients were managed by the Teletriage team with no onward referral, 57% were managed via community services e.g GPs, Community Geriatricians, and 10% were referred to the ambulance service. Emergency Health Care Plans (EHCPs), Preferred Priorities of Care and EOL (End of Life) wishes are taken into account.

Conclusions

The Teletriage project has reduced the number of phone calls to NHS 111 and the ambulance service, and subsequently has reduced the number of patients conveyed to hospital by 12%. The Teletriage nurses work very closely with various community services as well as GPs, NWAS and Community Geriatricians. The ongoing training and education provided to the Care Home Staff means that overall there has been good engagement with the project from the majority of the Wirral Care Homes.

Being Born Large for Gestational Age is Associated with Increased Global Placental DNA Methylation

Being born small (SGA) or large for gestational age (LGA) is associated with adverse birth outcomes and metabolic diseases in later life of the offspring. It is known that aberrations in growth during gestation are related to altered placental function. Placental function is regulated by epigenetic mechanisms such as DNA methylation. Several studies in recent years have demonstrated associations between altered patterns of DNA methylation and adverse birth outcomes. However, larger studies that reliably investigated global DNA methylation are lacking. The aim of this study was to characterize global placental DNA methylation in relationship to size for gestational age. Global DNA methylation was assessed in 1023 placental samples by LC-MS/MS. LGA offspring displayed significantly higher global placental DNA methylation compared to appropriate for gestational age (AGA; p < 0.001). ANCOVA analyses adjusted for known factors impacting on DNA methylation demonstrated an independent association between placental global DNA methylation and LGA births (p < 0.001). Tertile stratification according to global placental DNA methylation levels revealed a significantly higher frequency of LGA births in the third tertile. Furthermore, a multiple logistic regression analysis corrected for known factors influencing birth weight highlighted an independent positive association between global placental DNA methylation and the frequency of LGA births (p = 0.001).

Three patients with homozygous familial hypercholesterolemia: Genomic sequencing and kindred analysis

Background

Homozygous Familial Hypercholesterolemia (HoFH) is an inherited recessive condition associated with extremely high levels of low‐density lipoprotein (LDL) cholesterol in affected individuals. It is usually caused by homozygous or compound heterozygous functional mutations in the LDL receptor (LDLR). A number of mutations causing FH have been reported in literature and such genetic heterogeneity presents great challenges for disease diagnosis.

Objective

We aim to determine the likely genetic defects responsible for three cases of pediatric HoFH in two kindreds.

Methods

We applied whole exome sequencing (WES) on the two probands to determine the likely functional variants among candidate FH genes. We additionally applied 10x Genomics (10xG) Linked‐Reads whole genome sequencing (WGS) on one of the kindreds to identify potentially deleterious structural variants (SVs) underlying HoFH. A PCR‐based screening assay was also established to detect the LDLR structural variant in a cohort of 641 patients with elevated LDL.

Results

In the Caucasian kindred, the FH homozygosity can be attributed to two compound heterozygous LDLR damaging variants, an exon 12 p.G592E missense mutation and a novel 3kb exon 1 deletion. By analyzing the 10xG phased data, we ascertained that this deletion allele was most likely to have originated from a Russian ancestor. In the Mexican kindred, the strikingly elevated LDL cholesterol level can be attributed to a homozygous frameshift LDLR variant p.E113fs.

Conclusions

While the application of WES can provide a cost‐effective way of identifying the genetic causes of FH, it often lacks sensitivity for detecting structural variants. Our finding of the LDLR exon 1 deletion highlights the broader utility of Linked‐Read WGS in detecting SVs in the clinical setting, especially when HoFH patients remain undiagnosed after WES.

OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps

BACKGROUND

Optical mapping is an emerging technology that complements sequencing-based methods in genome analysis. It is widely used in improving genome assemblies and detecting structural variations by providing information over much longer (up to 1 Mb) reads. Current standards in optical mapping analysis involve assembling optical maps into contigs and aligning them to a reference, which is limited to pairwise comparison and becomes bias-prone when analyzing multiple samples.

FINDINGS

We present a new method, OMMA, that extends optical mapping to the study of complex genomic features by simultaneously interrogating optical maps across many samples in a reference-independent manner. OMMA captures and characterizes complex genomic features, e.g., multiple haplotypes, copy number variations, and subtelomeric structures when applied to 154 human samples across the 26 populations sequenced in the 1000 Genomes Project. For small genomes such as pathogenic bacteria, OMMA accurately reconstructs the phylogenomic relationships and identifies functional elements across 21 Acinetobacter baumannii strains.

CONCLUSIONS

With the increasing data throughput of optical mapping system, the use of this technology in comparative genome analysis across many samples will become feasible. OMMA is a timely solution that can address such computational need. The OMMA software is available at https://github.com/TF-Chan-Lab/OMTools.

Mitochondrial DNA mutation m.3243A>G is associated with altered mitochondrial function in peripheral blood mononuclear cells, with heteroplasmy levels and with clinical phenotypes

AIMS

To investigate the associations among heteroplasmy levels (i.e. the proportions of mutant and wild-type mitochondrial DNA in the same cell), mitochondrial function and clinical severity of the m.3243A>G mutation.

METHODS

A total of 17 participants carrying the m.3243A>G mutation and 17 sex- and age-matched healthy controls were included in this study. Heteroplasmy levels of the m.3243A>G mutation in leukocytes, saliva and urine sediment were determined by pyrosequencing. The clinical evaluation included endocrinological, audiological and ophthalmological examinations. Mitochondrial function was determined in peripheral blood mononuclear cells isolated from participants.

RESULTS

Heteroplasmy levels in urine sediment were higher than those in leukocytes and saliva. Reduced levels of adenosine triphosphate and mitochondrial membrane potential, and increased reactive oxygen species production were observed in mutant peripheral blood mononuclear cells (all P < 0.05). Linear regression analysis indicated that higher heteroplasmy levels in peripheral blood leukocytes were associated with increased levels of glycated albumin and HbA_1c , and decreased total hip bone mineral density T-score after adjustment for age and sex (all P < 0.05). Furthermore, mitochondrial membrane potential was independently associated with bone mineral density T-score at the femoral neck (P < 0.05).

CONCLUSIONS

Heteroplasmy levels in peripheral blood leukocytes and mitochondrial membrane potential in peripheral blood mononuclear cells were closely associated with clinical manifestations and were valuable for evaluation of the clinical severity of the m.3243A>G mutation.

Epididymal small non-coding RNA studies: progress over the past decade

BACKGROUND

Small non-coding RNAs (sncRNAs) accomplish a huge variety of biological functions. Over the past decade, we have witnessed the substantial progress in the epididymal sncRNA studies. In the Epididymis 7, we had the true privilege of having a whole session to share our findings and exchange ideas on the epididymal sncRNA studies.

OBJECTIVES

This mini-review attempts to provide an overview of what is known about the sncRNAs in the mammalian epididymis and discuss the future directions in this field.

METHODS

We surveyed literature regarding the sncRNA studies in the mammalian epididymis, and integrated some of our unpublished findings as well. We focus on the progress in methodology and the advances in our understanding of the expression and functions of epididymal sncRNAs.

RESULTS AND DISCUSSION

The applications of high-throughput approaches have made great contributions in the discovery of new sncRNA species and profiling their dynamics in the epithelial cells, the passing spermatozoa, and the luminal environment. The diverse classes of epididymal sncRNAs exert important biological functions from the in situ regulation of epididymal gene expression to the epigenetic inheritance in the offspring.

CONCLUSION

Although still in its infancy, we believe that the research on epididymal sncRNAs will not only lead to a better understanding of their physiological and pathological functions, but also contribute to the whole landscape of the RNA field.

Abstract P1-10-05: Analysis of genetic mutation in ethnically diverse population with Breast and ovarian cancer: Single institution experience

Only 5-10% of all breast and ovarian cancers have been attributed to inherited mutation. In unselected breast cancer patients, prevalence of germline BRCA 1 & 2 is about 2%. In Ashkenazi Jewish population the prevalence is estimated to be 11.7%. The rate of mutations in other populations has not been well characterized. The purpose of this study is to identify and characterize the risk of genetic mutations in an ethnically diverse population referred for genetic testing according to NCCN guidelines.

Method:

In this single institution retrospective study, we analyzed 782 patients referred for genetic testing between 2009-2018. Information regarding reason for referral, ethnicity, cancer history and results of genetic mutation using multigene panels were collected.

Results:

Reasons for referral were:

· Family History of cancer (142; 18.6%),

· Breast cancer diagnosed at early age (207; 26.4%),

· Triple negative breast cancer (12 ;53%

· Ovarian cancer (61; 7.8%)

· Multiple cancer (32; 4.09%)

· Known BRCA 1 or 2 mutation (51;6.5%)

· Known other mutation (9;1.15%)

· Family h/o cancer but not diagnosed with cancer (268)

Ethnic distribution:

· 328 Hispanic (41.94%)

· 177 Caucasian (22.6%),

· 27 Chinese, (3.4%)

· 52 Vietnamese (6.6%)

· 86 other- Asian (11%)

· 32 Middle eastern (4.1%),

· 14 South Asian (1.8%)

· 35 African American (4.5%)

· 8 Ashkenazi Jewish (1%)

· 19 Mixed Hispanic (2.1%)

Genetic testing was done in 545 /782 patients.

Deleterious Mutation detected: 88 patients (16.5% of tested)

· BRCA 1: 32(5.8%)

· BRCA 2:28 (5.14%)

· MSH2:5(0.9%)

· p53:39 (0.5%)

· PLB2:3 (0.38%)

· MUTYH:3 (0.38%)

· CDH1 :2 (0.26%)

· PMS2: 2 ( 0.26%)

· ATM: 1(0.13%)

· CCKn2A: 1(0.13%)

· CHEK 2: 1(0.13)

· MET:1(0.13%)

· MSH6:1 (0.13%)

· RAD50 :1(0.13%)

· RET1;1(0.13%)

BRCA1/BRCA2 mutation: 60

Mutation in BRCA 1/ 2 distribution by ethnicity:

· Hispanic (28; 8.54 %),

· Chinese (4;14.8%)

· Vietnamese (4; 7.7%)

· other Asian (12;13.9%)

· African American (3, 8.5, %)

· South Asian (0 %)

· Caucasian (8; 4.5 %)

· All Asian (20/165: 12.1%)

Mutation in other gene by Ethnicity: total 26

Hispanic (16, 4.5%), Caucasian: (3, 1.7%) Asian other than Chinese and Vietnamese (4, 4.65%)

Mutation in Breast cancer: 333 Breast cancer patients tested, 39 patients (11.17%) were found to have mutations.

10/32 triple negative (31%) 4/49 her2neu positive patients (8.1%) and 15/252 (5.9%) ER+ patients found to have mutations.

17/39 breast cancer patients with mutation had prophylactic BSO.

Mutation in BRCA 1& 2 by reason for referral:

Known family h/o of BRCA1 or 2 mutations (18; 39.5%)

Early age of cancer (10, 7.4%)

Cancer with positive family history (17, 8.2%)

Triple negative (2, 16%).

Variant of Unknown significance (VUS): 140 patients (25 %)

VUS in BRCA 2 were most common. VUS were found in 17% of Hispanic and African American patients.

No significant difference in PFS and OS was found in patient with mutation and without mutation

Conclusion:

We found much higher rates (16.5%) than previously reported mutation detection in this very highly diverse patient population.

Rate of BRCA 1&2 mutation was 8.55% in Hispanic and 12.1% in Asian patients compared with 4.5% in Caucasian patient when selected for high risk factors.

We Also noted very high rate of VUS especially in Hispanic and African American patients.

Citation Format: Aggarwal S, Chu C, Ngumi M. Analysis of genetic mutation in ethnically diverse population with Breast and ovarian cancer: Single institution experience [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-10-05.