Pilot Study of Return of Genetic Results to Patients in Adult Nephrology

Background and objectives: Actionable genetic findings have implications for care of patients with kidney disease, and genetic testing is an emerging tool in nephrology practice. However, there are scarce data regarding best practices for return of results and clinical application of actionable genetic findings for kidney patients. Design, setting, participants and measurements: We developed a Return of Results workflow in collaborations with clinicians for the retrospective re-contact of adult nephrology patients who had been recruited into a biobank research study for exome sequencing and were identified to have medically actionable genetic findings. Results: Using this workflow, we attempted to re-contact a diverse pilot cohort of 104 nephrology research participants with actionable genetic findings encompassing 34 different monogenic etiologies of nephropathy and five single-gene disorders recommended by the American College of Medical Genetics and Genomics for return as medically actionable secondary findings. We successfully re-contacted 64 (62%) participants and returned results to 41 (39%) individuals. In each case, the genetic diagnosis had meaningful implications for the patients’ nephrology care. Through implementation efforts and qualitative interviews with providers, we identified over 20 key challenges associated with returning results to study participants, and found that physician knowledge gaps in genomics was a recurrent theme. We iteratively addressed these challenges to yield an optimized workflow, which included standardized consultation notes with tailored management recommendations, monthly educational conferences on core topics in genomics, and a curated list of expert clinicians for cases requiring extra-nephrologic referrals. Conclusions: Developing the infrastructure to support return of genetic results in nephrology was resource-intensive, but presented potential opportunities for improving patient care

Multidisciplinary approaches for elucidating genetics and molecular pathogenesis of urinary tract malformations

Advances in clinical diagnostics and molecular tools have improved our understanding of the genetically heterogeneous causes underlying congenital anomalies of kidney and urinary tract (CAKUT). However, despite a sharp incline of CAKUT reports in the literature within the past 2 decades, there remains a plateau in the genetic diagnostic yield that is disproportionate to the accelerated ability to generate robust genome-wide data. Explanations for this observation include (i) diverse inheritance patterns with incomplete penetrance and variable expressivity, (ii) rarity of single-gene drivers such that large sample sizes are required to meet the burden of proof, and (iii) multigene interactions that might produce either intra- (e.g., copy number variants) or inter- (e.g., effects in trans) locus effects. These challenges present an opportunity for the community to implement innovative genetic and molecular avenues to explain the missing heritability and to better elucidate the mechanisms that underscore CAKUT. Here, we review recent multidisciplinary approaches at the intersection of genetics, genomics, in vivo modeling, and in vitro systems toward refining a blueprint for overcoming the diagnostic hurdles that are pervasive in urinary tract malformation cohorts. These approaches will not only benefit clinical management by reducing age at molecular diagnosis and prompting early evaluation for comorbid features but will also serve as a springboard for therapeutic development

Whole genome homozygosity mapping results.

<p>A red peak reaching a 1.0 max score of statistical significance depicts a homozygous region on chromosome 19. The region coincides with the 0.49 Mbp locus identified using two-point linkage analysis and is bracketed by recombination spots (indicated in red). The identified haploblock fulfills the zygosity criterion by displaying homozygosity in affected animals (indicated in red) and heterozygosity in unaffected carriers (indicated in green).</p

Sanger sequencing confirmation of the disease segregating variant identified in the linked region.

<p>Candidate region identified using linkage analysis in PACG pedigree animals (left). Sequence chromatograms from a carrier (C), confirms heterozygous genotype whereas affected animals (A) display a homozygous state of variant identified in <i>NEB</i> (g.5588214 A->G) (Right).</p

A Fisher exact contingency table of genotypes observed in a confirmatory animal cohort for the <i>RIF1</i> variant (g.55723957 C->T).

<p>Forty-four additional unaffected and affected Basset Hounds were selected for confirmatory sequencing of the <i>RIF1</i> variant (g.55723957 C->T). The observed total of individuals and percentage of individuals displaying a specific genotype is shown for each cell respectively. The two-tailed P value is 0.57 (Fisher Exact Probability Test)</p><p>A Fisher exact contingency table of genotypes observed in a confirmatory animal cohort for the <i>RIF1</i> variant (g.55723957 C->T).</p

A Fisher exact contingency table of genotypes observed in a confirmatory animal cohort for the <i>NEB</i> variant (g.55885214 A->G).

<p>Forty-four additional unaffected and affected Basset Hounds were selected for confirmatory sequencing of the <i>NEB</i> variant (g.55885214 A->G). The observed total of individuals and percentage of individuals displaying a specific genotype is shown for each cell respectively.</p><p>The two-tailed P value is 0.00034 (Fisher Exact Probability Test)</p><p>A Fisher exact contingency table of genotypes observed in a confirmatory animal cohort for the <i>NEB</i> variant (g.55885214 A->G).</p

Alignment of the amino acid sequence of exon 48 in Nebulin in several vertebrate species.

<p>The Lysine (K) residue (highlighted in blue) at position p.2051 is conserved among 23 vertebrate species.</p

Genome-wide linkage analysis of SNP genotype data.

<p>Using two-point linkage analysis, a maximum LOD_two-point score of 3.07 was achieved for a 0.49 Mb locus on chromosome 19. The red line of statistical significance indicates LOD scores values > 3 (A). Using multipoint linkage analysis, an increased maximum LOD_multipoint score of 3.24 was achieved for a locus mapped to the same location (B). A schematic view of the maximum LOD scores achieved across chromosome 19. The statistically significant locus is located at the distal end of chromosome 19 (Chr19: 54,949,124–56,765,346) and spans 1.82 Mbp (C).</p

Basset Hound Pedigree used in this study.

<p>The affected Basset 5a in the second generation was duplicated twice (5b and 5c) in order to break two otherwise computationally confounding breeding loops. Genotypes of typed markers within region uncovered following two-point linkage analysis are shown. Shading indicates the transmission pattern of heterozygous parental haplotypes to affected, homozygous offspring. Additional patterns of shading including diagonal lines indicate variation to the same haplotype identified in the other pedigree members. Complete concordance of homozygous haplotype inheritance with the disease phenotype is observed in all affected animals.</p