Rare Kidney Disease Registry and Biobank

Rare Kidney Disease Registry and Biobank

Irish Kidney Gene Project Biobank - Royal College of Surgeons in Ireland (rcsi.com)

Beaumont Hospital has partnered with the Royal College of Surgeons in Ireland to provide a Biobank for the storage of all clinical samples generated by the Irish Kidney Gene Project. The Biobank stores all samples in an anonymized fashion. Only Beaumont Hospital keeps track of the identity of samples. Samples are shared with clinical and investigational labs at the direction of clinical team at Beaumont Hospital .

For the past five years the Irish Kidney Gene Project (IKGP) group has been collecting DNA and clinical phenotype data from patients with a family history of kidney disease and patients who presented with kidney failure aged less than 50 where there was no clear underlying diagnosis. As mentioned, under the governance of the RKD Biobank and Registry, facilities are available for biobanking of DNA of affected individuals and appropriate affected and unaffected family members.

To date, clinical phenotyping and DNA collection has been performed on over 720 individual patients representing over 325 distinct pedigrees. The recruitment rate has increased exponentially since the project began in 2012 (Figure 1). The baseline clinical characteristics of recruited families are summarised in Table 1. 

                                                                                (Fig.1)

Current Projects

(1) Irish Kidney Gene Project - Prevalence of Familial Kidney Disease in Ireland.

This project involved interviews with 1800 Irish patients with chronic kidney disease at nephrology clinics and dialysis units nationwide . We observed a prevalence of family history of kidney disease amongst 34% of patients (or 27% when polycystic kidney disease cases were excluded). Familial kidney disease was particularly prevalent amongst those patients with Alport syndrome, Congenital Abnormalities of the Kidney and Urinary Tract (CAKUT), tubulointerstitial kidney disease and those with an uncertain aetiology.

This study highlighted the high prevalence of inherited kidney disease among our patients nationwide, and suggested that focused genetic analysis of certain groups was appropriate. This study was the foundation for the following studies all undertaken under the auspices of the IKGP group.

(2) Familial IgA Nephropathy

Fourteen families with familial IgA have been identified and recruited to IKGP. In this cohort, probable autosomal dominant and recessive modes of inheritance were observed. There were 42 affected individuals in the fourteen families (with either biopsy-proven IgA nephropathy or ESRD). A detailed clinical analysis of the patients and families has been accepted for publication by Nephron (Ref NEF-2017-7-14/R2).

Since this description, we have undertaken exome sequencing of ten of these families. In three out of the ten families we have identified candidate mutations. We identified collagen gene (COL4A3 and COL4A5) mutations in two families - one of which was definitely pathogenic and one likely pathogenic according to American College of Medical Genetics (ACMG standards) suggesting the alternate diagnosis of Alport Syndrome in these patients. In another family, we identified a mutation in the LMX1b gene which has previously been associated with Nail-patella syndrome, however further work is required to access the significance of this variant.

(3) Autosomal Dominant Tubulointerstitial Kidney Disease (ADTKD)

The IKGP database includes 49 patients from twelve families in Ireland with ADTKD. Of these, 19 patients, from three families, were demonstrated to have a pathogenic frameshift (cytosine insertion) MUC-1 mutation confirming the diagnosis to be ADTKD-MUC1. A further fourteen patients, from three families, are confirmed heterozygotes for a UMOD mutation, confirming ADTKD-UMOD. Each UMOD mutation led to a single amino acid substitution at protein level (tyrosine to cysteine substitution (p.Y274C), cysteine to tyrosine substitution (p.C223Y) and cysteine to tyrosine substitution (p.C106Y) respectively). All three mutations have been described in other families worldwide.  Investigations are pending for the remaining six families.

All in all, although likely under-recognised and under-diagnosed, this disease entity is thought to account for approximately 0.5% of Irish ESRD patients.

We have collaborated with Tony Bleyer in Bowman Grey University in North Carolina and the Broad Institute, Boston to make these observations. Our experience has been presented internationally and manuscript preparation is underway.

(4) Exome Sequencing of Irish Families with Undiagnosed Familial Kidney Failure

Autosomal Recessive inheritance

Hildbrandt/ Boston Children’s Hospital Collaboration 

Following establishment of the IKGP, and collaboration with the Rare Kidney Disease Biobank and Registry, we commenced a collaborative project with the Renal Genetics Laboratory Harvard, Boston. This project involves close collaboration with Dr Dervla Connaughton, research fellow in Beaumont Hospital/Boston Children’s Hospital working in conjunction with Dr Friedhelm Hildebrandt.

The primary aim of this collaboration is to identify the underlying causative molecular defects in individuals with kidney disease through whole exome sequencing analysis. Following phenotyping of individuals recruited to the IKGP in Ireland, we then proceed with genetic analysis and interpretation at the Renal Genetic Laboratory in Boston. We hypothesize that analysis of the phenotypic variants of kidney disease will allow for sub classification, thus facilitating further characterization and genetic analysis.

To date, whole exome sequencing analysis has been performed on DNA samples from 151 individuals from 109 Irish families. These families are largely believed to be recessive in their pattern of inheritance.

Analysis is complete for 31 individuals from 16 families. This has allowed establishment of a molecular diagnosis in 50% of families (8/16 families, 12 individuals). The molecular diagnoses made in this research capacity to date include:

• Three siblings (one deceased) with ESRD in the setting of nephronophthisis and retinal dystrophy were identified as homozygotes for an IFT140 gene mutation, chromosome 16. This gene is highly expressed in the retina and kidney and is essential for maintenance of normal ciliary health and function.

• Two siblings with ESRD of uncetain aetiology, with mildly deranged liver function tests and a propensity to cancer were found to be compound heterozygotes for a FAN1 gene mutation (chromosome 15). This gene encodes a DNA repair nuclease; mutations of which lead to a karyomegalic interstitial nephritis.

Several of these have been confirmed in a diagnostic laboratory; others are pending confirmation. This work was presented at the American Society of Nephrology meeting, 2017.

We plan to continue recruitment of individuals with kidney disease for the duration of this project. We have already developed significant infrastructure and expertise at the Clinical Research Centre at Beaumont Hospital, which will facilitate ongoing recruitment and further expansion of this project.

(5) Exome Sequencing of Irish Families with Undiagnosed Familial Kidney Failure

Autosomal Dominant Inheritance

Gbadegesin/Duke Collaboration

We have also established a collaboration with Dr Rasheed Gbadegesin at Duke University NC USA  to look at genes involved in autosomal dominant patterns of inheritance. Rasheed has undertaken exome sequencing and gene linkage studies on 5 Irish families with novel genes involved in kidney disease not previously described.

Active collaborative family studies ar ongoing on one large Irish pedigree recruited under the IKGP umbrella with familial spastic paraparesis and chronic kidney disease (n=21 family members with DNA collection); another large family with autosomal dominant inheritance pattern of FSGS (n=22 family members with DNA collection) and a third large family with familial glomerulonephritis (n=10 family members with DNA collection).

(6) Exome Sequencing of Irish Families with Undiagnosed Familial Kidney Failure

 Cavalleri / Benson/RCSI Collaboration

We have undertaken both exome sequencing and targeted gene sequencing using custom Roche sequencing panels in the Cavalleri Lab at RCSI. A custom targeted panel is used to diagnose hereditary renal disease patients with presentation of kidney disease at <30years of age or in a family with ≥2 members with stage 3 chronic kidney disease or higher. In patients with an extensive pedigree chart with multiple="multiple" affected family members, where no molecular diagnosis was made with the targeted panel, exome sequencing was used in selected="selected" cases to further elucidate the cause of the family’s disease.

Initially, we used a Roche HeatSeq targeted panel to sequence hereditary renal disease patients using an amplification based preparation approach. This preliminary test panel aimed to estimate the potential yield of targeted sequencing in an Irish cohort of renal disease patients. The panel targeted 11 established renal disease genes and was used to sequence 88 patients on the Illumina MiSeq .We were successful in establishing a likely molecular diagnosis in 26% (23/88) of these patients.

The hybridisation-based custom targeted sequencing panel (Roche SeqCap) has now been designed. This new panel has a larger target size (227 genes). Previous literature has shown that this type of hybridisation based library preparation can be used to successfully target the PKD1 gene despite the presence of the potentially confounding pseudogenes. We aim to test this panel on 8 patients before Christmas 2017 using the Illumina MiSeq and then to sequence a further 96 patients in January/February 2018 on the Illumina NextSeq which is hosted at UCD.