Mutations causing medullary cystic kidney disease type 1 (MCKD1) lie in a large VNTR in MUC1 missed by massively parallel sequencing

While genetic lesions responsible for some Mendelian disorders can be rapidly discovered through massively parallel sequencing (MPS) of whole genomes or exomes, not all diseases readily yield to such efforts. We describe the illustrative case of the simple Mendelian disorder medullary cystic kidney disease type 1 (MCKD1), mapped more than a decade ago to a 2-Mb region on chromosome 1. Ultimately, only by cloning, capillary sequencing, and de novo assembly, we found that each of six MCKD1 families harbors an equivalent, but apparently independently arising, mutation in sequence dramatically underrepresented in MPS data: the insertion of a single C in one copy (but a different copy in each family) of the repeat unit comprising the extremely long (~1.5-5 kb), GC-rich (>80%), coding VNTR in the mucin 1 gene. The results provide a cautionary tale about the challenges in identifying genes responsible for Mendelian, let alone more complex, disorders through MPS

Mutations causing medullary cystic kidney disease type 1 (MCKD1) lie in a large VNTR in MUC1 missed by massively parallel sequencing

While genetic lesions responsible for some Mendelian disorders can be rapidly discovered through massively parallel sequencing (MPS) of whole genomes or exomes, not all diseases readily yield to such efforts. We describe the illustrative case of the simple Mendelian disorder medullary cystic kidney disease type 1 (MCKD1), mapped more than a decade ago to a 2-Mb region on chromosome 1. Ultimately, only by cloning, capillary sequencing, and de novo assembly, we found that each of six MCKD1 families harbors an equivalent, but apparently independently arising, mutation in sequence dramatically underrepresented in MPS data: the insertion of a single C in one copy (but a different copy in each family) of the repeat unit comprising the extremely long (~1.5-5 kb), GC-rich (>80%), coding VNTR in the mucin 1 gene. The results provide a cautionary tale about the challenges in identifying genes responsible for Mendelian, let alone more complex, disorders through MPS

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing

Although genetic lesions responsible for some mendelian disorders can be rapidly discovered through massively parallel sequencing of whole genomes or exomes, not all diseases readily yield to such efforts. We describe the illustrative case of the simple mendelian disorder medullary cystic kidney disease type 1 (MCKD1), mapped more than a decade ago to a 2-Mb region on chromosome 1. Ultimately, only by cloning, capillary sequencing and de novo assembly did we find that each of six families with MCKD1 harbors an equivalent but apparently independently arising mutation in sequence markedly under-represented in massively parallel sequencing data: the insertion of a single cytosine in one copy (but a different copy in each family) of the repeat unit comprising the extremely long (~1.5–5 kb), GC-rich (>80%) coding variable-number tandem repeat (VNTR) sequence in the MUC1 gene encoding mucin 1. These results provide a cautionary tale about the challenges in identifying the genes responsible for mendelian, let alone more complex, disorders through massively parallel sequencing.National Institutes of Health (U.S.) (Intramural Research Program)National Human Genome Research Institute (U.S.)Charles University (program UNCE 204011)Charles University (program PRVOUK-P24/LF1/3)Czech Republic. Ministry of Education, Youth, and Sports (grant NT13116-4/2012)Czech Republic. Ministry of Health (grant NT13116-4/2012)Czech Republic. Ministry of Health (grant LH12015)National Institutes of Health (U.S.) (Harvard Digestive Diseases Center, grant DK34854

Nephrocalcinosis (enamel renal syndrome) caused by autosomal recessive FAM20A mutations

Calcium homeostasis requires regulated cellular and interstitial systems interacting to modulate the activity and movement of this ion. Disruption of these systems in the kidney results in nephrocalcinosis and nephrolithiasis, important medical problems whose pathogenesis is incompletely understood

Effects of Sex on Intra-Individual Variance in Urinary Solutes in Stone-Formers Collected from a Single Clinical Laboratory

<div><p>Background/Aims</p><p>Our work in a rodent model of urinary calcium suggests genetic and gender effects on increased residual variability in urine chemistries. Based on these findings, we hypothesized that sex would similarly be associated with residual variation in human urine solutes. Sex-related effects on residuals might affect the establishment of physiological baselines and error in medical assays.</p><p>Methods</p><p>We tested the effects of sex on residual variation in urine chemistry by estimating coefficients of variation (<i>CV</i>) for urinary solutes in paired sequential 24-h urines (≤72 hour interval) in 6,758 females and 9,024 males aged 16–80 submitted to a clinical laboratory.</p><p>Results</p><p>Females had higher <i>CV</i>s than males for urinary phosphorus overall at the False Discovery Rate (<i>P</i><0.01). There was no effect of sex on <i>CV</i> for calcium (<i>P</i>>0.3). Males had higher <i>CV</i>s for citrate (<i>P</i><0.01) from ages 16–45 and females higher <i>CV</i>s for citrate (<i>P</i><0.01) from ages 56–80, suggesting effects of an extant oestral cycle on residual variance.</p><p>Conclusions</p><p>Our findings indicate the effects of sex on residual variance of the excretion of urinary solutes including phosphorus and citrate; differences in <i>CV</i> by sex might reflect dietary lability, differences in the fidelity of reporting or genetic differentiation in renal solute consistency. Such an effect could complicate medical analysis by the addition of random error to phenotypic assays. Renal analysis might require explicit incorporation of heterogeneity among factorial effects, and for sex in particular.</p></div

Effects of sex-by-age category (16–45 years <i>vs</i>. 56–80 years) interaction on ranked coefficients of variation (<i>CV</i> = <i>σ/μ</i>) calculated from original paired 24-h urinary solutes (urinary ammonium (NH₃), calcium (Ca), chloride (Cl), citrate (Cit), potassium (K), magnesium (Mg), sodium (Na), oxalate (Ox), phosphorus (P), sulfate (SO₄), uric acid (UA), urine urea nitrogen (UN)) collected from 6,758 female and 9,024 male stone-formers aged 16–80 at the False Discovery Rate [Verhoeven, 2005 #22836].

<p>Effects of sex-by-age category (16–45 years <i>vs</i>. 56–80 years) interaction on ranked coefficients of variation (<i>CV</i> = <i>σ/μ</i>) calculated from original paired 24-h urinary solutes (urinary ammonium (NH₃), calcium (Ca), chloride (Cl), citrate (Cit), potassium (K), magnesium (Mg), sodium (Na), oxalate (Ox), phosphorus (P), sulfate (SO₄), uric acid (UA), urine urea nitrogen (UN)) collected from 6,758 female and 9,024 male stone-formers aged 16–80 at the False Discovery Rate [Verhoeven, 2005 #22836].</p

Effects of gender on ranked coefficients of variation (<i>CV</i>) from paired 24-h urinary measurements of urinary ammonium (NH₃), calcium (Ca), chloride (Cl), citrate (Cit), potassium (K), magnesium (Mg), sodium (Na), oxalate (Ox), phosphorus (P), sulfate (SO₄), uric acid (UA) and urine urea nitrogen (UN) adjusted for creatinine, urinary volume, age and weight in the complete population of 6,758 females and 9,024 males aged 16–80, and in individuals aged 16–45 and 56–80 in a stepwise backward regression (<i>P</i>_acceptance≤0.1).

<p>Significance (below) is corrected for multiple observations via False Discovery Rate [Verhoeven, 2005 #22836]. Nominal <i>P</i>-value (<i>P</i>_nom) is reported at acceptance or removal from the model during the stepwise procedure. Units indicates original values used in <i>CV</i> calculation.</p><p><i>P</i>_nom = nominal <i>P</i>-value.</p>*<p><i>P</i>_FDR<0.05,</p>**<p><i>P</i>_FDR<0.01.</p><p>Correlation coefficients (<i>r</i>²) refer to the complete model correlation, or model fit at rejection of nonsignificant terms via backwards regression (removal at <i>P</i>>0.1).</p><p>Negative <i>β</i> indicates lower female <i>CV</i>; positive <i>β</i> higher male CV.</p