Intestinal Microbiota and Host Cooperate for Adaptation as a Hologenome

The hologenome concept has broadened our perspectives for studying host-microbe coevolution. The multiomic analyses reported here involved two lines of chickens, from a common founder population, that had undergone long-term selection for high (HWS) or low (LWS) 56-day body weight.

A Common Founder Effect of the Splice Site Variant c.-23+1G>A in GJB2 Gene Causing Autosomal Recessive Deafness 1A (DFNB1A) in Eurasia

The mutations in the GJB2 gene are known to be a major cause of autosomal recessive deafness 1A (OMIM 220290). The most common pathogenic variants of the GJB2 gene have high ethno-geographic specificity in their distribution that being attributed to a founder effect related with Neolithic migration routes of Homo sapiens. Curiously, the c.-23+1G>A splice site variant is frequently found among deaf patients of both Caucasian and Asian origin. It is currently unknown whether this mutation did spread across Eurasia as a result of the founder effect or it could have multiple local centers of origin. To determine the origin of the c.-23+1G>A we reconstructed 𝑓2-haplotypes by genotyping SNPs on the Illumina OmniExpress 730K platform in 23 deaf individuals homozygous for this variant from different populations of Eurasia (Yakuts, Tuvinians, Evenk, Kumyk, Armenian, Russians and Slovak). The analysis revealed that the homozygosity regions in different individuals overlapped in one short region with the length of ~5.2 kb. These data support the hypothesis of the common founder effect in distribution of the c.-23+1G>A variant of GJB2 gene. Based on the published data on the c.-23+1G>A prevalence among 16,177 deaf people and calculation of TMRCA of the 𝑓2-haplotypes carrying this variant we reconstructed the potential migration routes of the c.-23+1G>A carriers around the world. This analysis indicates that the c.-23+1G>A variant may have originated approximately 6,000 years ago in the territory of the Caucasus or Middle East, followed by spread throughout Europe, South and Central Asia and other regions of the world.

In Silico identification of a common mobile element insertion in exon 4 of RP1

Mobile element insertions (MEIs) typically exceed the read lengths of short-read sequencing technologies and are therefore frequently missed. Recently, a founder Alu insertion in exon 4 of RP1 has been detected in Japanese patients with macular dystrophy by PCR and gel electrophoresis. We aimed to develop a grep search program for the detection of the Alu insertion in exon 4 of RP1 using unprocessed short reads. Among 494 unrelated Korean patients with inherited eye diseases, 273 patients with specific retinal phenotypes who were previously genotyped by targeted panel or whole exome sequencing were selected. Five probands had a single heterozygous truncating RP1 variant, and one of their unaffected parents also carry this variant. To find a hidden genetic variant, whole genome sequencing was performed in two patients, and it revealed AluY c.4052_4053ins328/p.(Tyr1352Alafs*9) insertion in RP1 exon 4. This AluY insertion was additionally identified in other 3 families, which was confirmed by PCR and gel electrophoresis. We developed simplified grep search program to detect this AluY insertion in RP1 exon 4. The simple grep search revealed a median variant allele frequency of 0.282 (interquartile range, 0.232–0.383), with no false-positive results using 120 control samples. The MEI in RP1 exon 4 was a common founder mutation in Korean, occurring in 1.8% of our cohort. The RP1-Alu grep program efficiently detected the AluY insertion, without the preprocessing of raw data or complex installation processes.

Rising of LOXHD1 as a signature causative gene of down-sloping hearing loss in people in their teens and 20s

BackgroundDown-sloping sensorineural hearing loss (SNHL) in people in their teens and 20s hampers efficient learning and communication and in-depth social interactions. Nonetheless, its aetiology remains largely unclear, with the exception of some potential causative genes, none of which stands out especially in people in their teens and 20s. Here, we examined the role and genotype–phenotype correlation of lipoxygenase homology domain 1 (LOXHD1) in down-sloping SNHL through a cohort study.MethodsBased on the Seoul National University Bundang Hospital (SNUBH) genetic deafness cohort, in which the patients show varying degrees of deafness and different onset ages (n=1055), we have established the ‘SNUBH Teenager–Young Adult Down-sloping SNHL’ cohort (10–35 years old) (n=47), all of whom underwent exome sequencing. Three-dimensional molecular modelling, minigene splicing assay and short tandem repeat marker genotyping were performed, and medical records were reviewed.ResultsLOXHD1 accounted for 33.3% of all genetically diagnosed cases of down-sloping SNHL (n=18) and 12.8% of cases in the whole down-sloping SNHL cohort (n=47) of young adults. We identified a potential common founder allele, as well as an interesting genotype–phenotype correlation. We also showed that transcript 6 is necessary and probably sufficient for normal hearing.ConclusionsLOXHD1 exceeds other genes in its contribution to down-sloping SNHL in young adults, rising as a signature causative gene, and shows a potential but interesting genotype–phenotype correlation.

A novel frequent BRCA1 recurrent variant c.5117G > A (p.Gly1206Glu) identified after 20 years of BRCA1/2 research in the Baltic region: cohort study and literature review

Background Several recent studies in the Baltic region have found extended spectrum of pathogenic variants (PV) of the BRCA1/2 genes. The aim of current study is to analyze the spectrum of the BRCA1/2 PV in population of Latvia and to compare common PV between populations of the Baltic region. Methods We present a cohort of 9543 unrelated individuals including ones with cancer and unaffected individuals from population of Latvia, who were tested for three most common BRCA1 founder PV. In second line testing, 164 founder negative high-risk individuals were tested for PV of the BRCA1/2 using next generation sequencing (NGS). Local spectrum of the BRCA1/2 PV was compared with the Baltic region by performing a literature review. Results Founder PV c.5266dupC, c.4035delA or c.181 T > G was detected in 369/9543 (3.9%) cases. Other BRCA1/2 PV were found in 44/164 (26.8%) of NGS cases. Four recurrent BRCA1 variants c.5117G > A (p.Gly1706Glu), c.4675G > A (p.Glu1559Lys), c.5503C > T (p.Arg1835*) and c.1961delA (p.Lys654fs) were detected in 18/44 (41.0%), 5/44 (11.4%), 2/44 (4.5%) and 2/44 (4.5%) cases respectively. Additionally, 11 BRCA1 PV and six BRCA2 PV were each found in single family. Conclusions By combining three studies by our group of the same cohort in Latvia, frequency of the BRCA1/2 PV for unselected breast and ovarian cancer cases is 241/5060 (4.8%) and 162/1067 (15.2%) respectively. The frequency of three “historical” founder PV is up to 87.0% (369/424). Other non-founder PV contribute to at least 13.0% (55/424) and this proportion probably will rise by increasing numbers of the BRCA1/2 sequencing. In relative numbers, c.5117G > A is currently the third most frequent PV of the BRCA1 in population of Latvia, overcoming previously known third most common founder variant c.181 T > G. In addition to three BRCA1 founder PV, a total of five recurrent BRCA1 and two recurrent BRCA2 PV have been reported in population of Latvia so far. Many of the BRCA1/2 PV reported in Latvia are shared among other populations of the Baltic region.

Prevalence of hereditary transthyretin cardiac amyloidosis (mATTR) in Western Denmark

Purpose To investigate the prevalence of mATTR in a cohort of consecutive ATTR patients in a tertiary Danish Amyloidosis Center. Methods Consecutive patients in the period from 2001 to 2019 with a definite diagnosis of ATTR-CA or ATTR-FAP based on either 99-Tc-DPD-scintigraphy, or transthyretin deposition in the myocardium or fatty tissue proved by immunohistology or protein mass spectrometry underwent testing for exonic genetic TTR variants. The distributions of age at time of diagnosis of mATTR and wildtype ATTR (wtATTR) are described by mean age, standard deviations, and range. Results Seventy-four caucasian patients of Danish ancestry except one (Swedish) with ATTR were included (72 ATTR-CA, 2 ATTR-FAP). TTR missense variants were present in 13.5% (10/74) of ATTR patients concluded to have mATTR: c.148G>A/p.Val50Met, n=1; c.187C>T/p.Pro63Ser, n=1; c.193G>T/p.Ala65Ser, n=2; c.218G>C; p.Gly73Ala, n=1; c.391C>A/p.Leu131Met, n=3; c.424G>A/p.Val142Ile, n=2. The mean age of mATTR patients was 57.6 years ±13.0, range 37.1–71.3 years, and was significantly lower than mean age for wtATTR patients: 79.4 years ±5.5, range 65.7–90.2 years, p=0.0004 (Welch's two-sample t-test with unequal variances). All patients with mATTR had familial disease proven by clinical phenotyping of family members or had a positive family history with heart failure and pacemaker use. Conclusion A minority of Danish patients (10–15%) with ATTR have mATTR. These mATTR patients are characterised by a significantly younger age at time of diagnosis than wtATTR patients. This observation indicates that TTR gene test may not be necessary in ATTR in patients older than 75 years. For the first time, the p.Val142Ile TTR variant, associated with mATTR and prevalent in 4% of African-Americans, was identified in a Danish family with mATTR-CA – a finding that may be explained by a common founder effect. Funding Acknowledgement Type of funding source: None

Absence of a common founder mutation in patients with co-occurring myelodysplastic syndrome and plasma cell disorder

Epidemiological studies have demonstrated an increased incidence of MDS in patients with plasma cell disorder (PCD) i.e. multiple myeloma (MM) or MGUS and several case reports / series of co-occurring MDS and PCD have been published. The underlying pathogenesis for this condition, and if the two diseases share a common genetic lesion remains unknown. Here, we describe a cohort of 27 consecutive patients with co-occurring MDS and MM (n=6), MGUS (n=20) or plasmocytoma (n=1), diagnosed at the Karolinska University Hospital. In 5 patients, the diagnosis of MGUS preceded the diagnosis of MDS , in one patient the MDS diagnosis preceded PCD, and in 21 patients MDS and PCD were diagnosed at the same time. There was a preponderance for lower-risk MDS subgroups with only 3 patients belonging to the IPSS-R high / very high risk groups. Median overall survival for the whole cohort was 44 months. The most common mutations were TET2, SRSF2 and SF3B1. To identify potential common founder clones, we performed whole exome sequencing on isolated bone marrow myeloid-, plasma- and T-cells from 9 patients. In none of the patients, we could detect a common founder mutation and the two diseases have likely emerged from separate clones.