Analytical validation of a novel comprehensive genomic profiling informed circulating tumor DNA monitoring assay for solid tumors

Emerging technologies focused on the detection and quantification of circulating tumor DNA (ctDNA) in blood show extensive potential for managing patient treatment decisions, informing risk of recurrence, and predicting response to therapy. Currently available tissue-informed approaches are often limited by the need for additional sequencing of normal tissue or peripheral mononuclear cells to identify non-tumor-derived alterations while tissue-naïve approaches are often limited in sensitivity. Here we present the analytical validation for a novel ctDNA monitoring assay, FoundationOne®Tracker. The assay utilizes somatic alterations from comprehensive genomic profiling (CGP) of tumor tissue. A novel algorithm identifies monitorable alterations with a high probability of being somatic and computationally filters non-tumor-derived alterations such as germline or clonal hematopoiesis variants without the need for sequencing of additional samples. Monitorable alterations identified from tissue CGP are then quantified in blood using a multiplex polymerase chain reaction assay based on the validated SignateraTM assay. The analytical specificity of the plasma workflow is shown to be 99.6% at the sample level. Analytical sensitivity is shown to be >97.3% at ≥5 mean tumor molecules per mL of plasma (MTM/mL) when tested with the most conservative configuration using only two monitorable alterations. The assay also demonstrates high analytical accuracy when compared to liquid biopsy-based CGP as well as high qualitative (measured 100% PPA) and quantitative precision (<11.2% coefficient of variation).

Abdominal wall calcification in a peritoneal dialysis patient

Abdominal wall calcification in a peritoneal dialysis patient has not previously been reported. We describe a 40-year-old lady, a type 2 diabetic and hypertensive for the past 14 years, who did not have any history, clinical features or laboratory results suggesting autoimmune disease, and had not suffered from tuberculosis in the past, but who had been diagnosed with chronic kidney disease in 2016. She had initiated peritoneal dialysis in December 2018.

Socioeconomic inequality among smoking and smokeless tobacco uses among males in India: a decomposition analysis

OBJECTIVE

India is the third-largest tobacco manufacturer and its use in India is characterised by a high prevalence of smoking and smokeless (sl) tobacco use. This results in 1 million deaths per year in the country. Given the high burden of tobacco use, this study examines the regional variations and socio-economic correlates of tobacco use in India.

METHODS

National Family Health Survey- 5 (2019-2020) have been analysed for the purpose of the study. A sample of 101,839 males aged 15-54 years was included in this study. Primary outcomes of tobacco use were categorised into smoking, smokeless and dual use of smoking and smokeless tobacco use. Bivariate analysis and decomposition analysis was done to study the socio-economic inequality.

RESULTS

The prevalence of tobacco use among males in India is around 41 percent. As indicated by the results of the logistics regression, age is positively related to smoking among males. Males aged 45-54 years are 2.5 (95 % concentration index [CI]:2.30-2.63) times probable to smoke, 1.4 (95% CI: 1.30-1.47) times probable of smokeless tobacco consumption and 2.2 (95% CI: 2.10-2.35) times more prone to using both types of substances compared to the younger age group. Males who are widower use smokeless 1.69 times (95% CI: 1.44-1.99) higher with reference to unmarried males. Males belonging to Scheduled tribes are 1.2 (95% CI: 1.13-1.25) times more likely to smoke, 1.3 (95% CI: 1.24-1.37) times more likely to use smokeless substances and 1.4 (95% CI: 1.33-1.47) times more likely to have dual use of tobacco than other social groups. Manual workers (both skilled are unskilled) are likely to smoke (odds ratio [OR] = 1.1, 95% CI: 1.02-1.11), use smokeless tobacco (OR = 1.3, 95% CI: 1.23-1.34) and have dual use of tobacco (OR = 1.29, 95% CI: 1.24-1.34) more than that of other categories. The decomposition of the concentration index shows a significant contribution from factors like a no education, ST/SC caste and wealth index. Among the states and union territories, the prevalence of tobacco is high in West Bengal, Tripura, Mizoram, Manipur, Meghalaya and Sikkim.

CONCLUSION

This study is useful for informing target-based prevention policies since it helps in highlighting regions, socio-economic and demographic groups especially vulnerable to tobacco addiction. In India, males from poorer and vulnerable socio-economic backgrounds are more likely to use tobacco. State wise, the eastern zone starting from West Bengal to the North-Eastern states have higher tobacco use than the rest of the country. There is an urgent need to frame policies for controlling the use of tobacco especially among high-risk groups.

Correlation between variant allele frequency and mean tumor molecules with tumor burden in patients with solid tumors

Several studies have demonstrated the prognostic value of circulating tumor DNA (ctDNA); however, the correlation of mean tumor molecules (MTM)/ml of plasma and mean variant allele frequency (mVAF; %) with clinical parameters is yet to be understood. In this study, we analyzed ctDNA data in a pan-cancer cohort of 23 543 patients who had ctDNA testing performed using a personalized, tumor-informed assay (Signatera™, mPCR-NGS assay). For ctDNA-positive patients, the correlation between MTM/ml and mVAF was examined. Two subanalyses were performed: (a) to establish the association of ctDNA with tumor volume and (b) to assess the correlation between ctDNA dynamics and patient outcomes. On a global cohort, a positive correlation between MTM/ml and mVAF was observed. Among 18 426 patients with longitudinal ctDNA measurements, 13.3% had discordant trajectories between MTM/ml and mVAF at subsequent time points. In metastatic patients receiving immunotherapy (N = 51), changes in ctDNA levels expressed both in MTM/ml and mVAF showed a statistically significant association with progression-free survival; however, the correlation with MTM/ml was numerically stronger.

COVID-19 disease in peritoneal dialysis patients: a single centre experience from India

BACKGROUND

This study presents our data on mortality in end stage renal disease (ESRD) patients on peritoneal dialysis (PD) who developed COVID-19.

MATERIALS AND METHODS

Sri Padmavathi Medical College Hospital, Sri Venkateswara Institute of Medical Sciences University, was designated the State COVID Hospital in March 2020. In a retrospective observational study, we collected the data of ESRD patients on PD and identified the risk factors for mortality.

RESULTS

Prior to the pandemic, 136 patients with ESRD were on peritoneal dialysis at our Institute. Among them, 27 (19.8%) eventually developed COVID-19, and 14 of them (51.8%) died. Serum albumin levels were lower and D-dimer levels were significantly higher in deceased patients than in survivors.

DISCUSSION

The mortality rate in ESRD patients on PD with COVID-19 at our institution was higher than in other published studies.

Water drinking practices in adpkd patients: A questionnaire based study

Introduction:

Patients with autosomal dominant polycystic kidney disease (ADPKD) who have normal renal function (creatinine clearance, >90 ml per minute per 1.73 m² of body-surface area) might potentially benefit from frequent water intake that would be sufficient to reduce plasma AVP levels and decrease the average urine osmolality, bringing it closer to that of plasma.

Materials and Methods:

In this cross-sectional study, the patients of ADPKD, chronic kidney disease stages 1–5 were included. We formed a questionnaire on the dietary recommendation to the patients. The questions enquired whether the patients received the recommendation from the faculty and the postgraduates of the nephrology department that (a) they should consume at least 3000 mL of water per day, (b) that they should not consume coffee and tea,(c) adherence of patients to the advice of the nephrologists.

Results:

Of 294 patients, 142 (48.2%) did not receive any dietary recommendation. The rest 152 (51.7%) were given the appropriate dietary recommendation. Majority of the patients mentioned that they lacked the access to the water when they intend to consume. Despite the advice from the nephrologists, 95 (32.3%) failed to observe the abstinence from coffee and tea. The reason expressed for not quitting coffee and tea was the force of the habit.

Conclusion:

Treating doctorsfailed to inform 48% of patients the proper diet. Only 20.3% of patients consumed >3.0 litre of water per day. The demand of the agricultural work at a place away from home deprived majority of the participants of the study from the potable water.

Nephrology Postgraduate Training in Peritoneal Dialysis: An Online Survey

Introduction:

One of the reasons for the peritoneal dialysis (PD) underutilization is related to the training of nephrology postgraduates in PD. This notion is not yet investigated in our country.

Methods:

We gathered the emails of the heads of the departments of nephrology of all medical colleges and the institutes, which impart DM nephrology post-graduation. We sent the questionnaire framed on the postgraduate training of PD. We received the questionnaire responses anonymously. The broad headings in the questionnaire are information on training resources, training activities, perceived adequacy of the training, and the factors, which limit the utilization of PD.

Results:

There are 42 medical colleges and institutes (excluding Sri Venkateswara Institute of Medical Sciences) that impart DM nephrology post-graduation in our country. Of these, 30 heads of the departments had responded. More than half of the heads of the department felt that the PD training postgraduates were inadequate. When asked to describe the reason for the perceived inadequacy of PD training, the primary reason noted included was insufficient numbers of PD patients (66.67%).

Discussion:

The conclusion may be drawn from our study that the postgraduate training in PD in our country is gratifying. Our hypothesis that a lacuna in postgraduate training in PD may be one of the reasons for the underutilization of PD seems ungrounded.

Rhabdomyolysis due to hypothyroidism without any precipitating factor

Rhabdomyolysis may develop due to hypothyroidism alone without any precipitating factors, but such reports are rare. We report as such the first manifestation of hypothyroidism.

Analytical Validation of a Single-nucleotide Polymorphism-based Donor-derived Cell-free DNA Assay for Detecting Rejection in Kidney Transplant Patients

BACKGROUND

Early detection of rejection in kidney transplant recipients holds the promise to improve clinical outcomes. Development and implementation of more accurate, noninvasive methods to detect allograft rejection remain an ongoing challenge. The limitations of existing allograft surveillance methods present an opportunity for donor-derived cell-free DNA (dd-cfDNA), which can accurately and rapidly differentiate patients with allograft rejection from patients with stable organ function.

METHODS

This study evaluated the analytical performance of a massively multiplexed polymerase chain reaction assay that targets 13 962 single-nucleotide polymorphisms, characterized and validated using 66 unique samples with 1064 replicates, including cell line-derived reference samples, plasma-derived mixtures, and transplant patient samples. The dd-cfDNA fraction was quantified in both related and unrelated donor-recipient pairs.

RESULTS

The dd-cfDNA assay showed a limit of blank of 0.11%, a limit of detection and limit of quantitation of 0.15% for unrelated donors, and limit of blank of 0.23%, a limit of detection and limit of quantitation of 0.29% for related donors. All other metrics (linearity, accuracy, and precision) were observed to be equivalent between unrelated and related donors. The measurement precision of coefficient of variation was 1.8% (repeatability, 0.6% dd-cfDNA) and was <5% for all the different reproducibility measures.

CONCLUSIONS

This study validates the performance of a single-nucleotide polymorphism-based massively multiplexed polymerase chain reaction assay to detect the dd-cfDNA fraction with improved precision over currently available tests, regardless of donor-recipient relationships.

Early Detection of Metastatic Relapse and Monitoring of Therapeutic Efficacy by Ultra-Deep Sequencing of Plasma Cell-Free DNA in Patients With Urothelial Bladder Carcinoma

PURPOSE

Novel sensitive methods for early detection of relapse and for monitoring therapeutic efficacy may have a huge impact on risk stratification, treatment, and ultimately outcome for patients with bladder cancer. We addressed the prognostic and predictive impact of ultra-deep sequencing of cell-free DNA in patients before and after cystectomy and during chemotherapy.

PATIENTS AND METHODS

We included 68 patients with localized advanced bladder cancer. Patient-specific somatic mutations, identified by whole-exome sequencing, were used to assess circulating tumor DNA (ctDNA) by ultra-deep sequencing (median, 105,000×) of plasma DNA. Plasma samples (n = 656) were procured at diagnosis, during chemotherapy, before cystectomy, and during surveillance. Expression profiling was performed for tumor subtype and immune signature analyses.

RESULTS

Presence of ctDNA was highly prognostic at diagnosis before chemotherapy (hazard ratio, 29.1; P = .001). After cystectomy, ctDNA analysis correctly identified all patients with metastatic relapse during disease monitoring (100% sensitivity, 98% specificity). A median lead time over radiographic imaging of 96 days was observed. In addition, for high-risk patients (ctDNA positive before or during treatment), the dynamics of ctDNA during chemotherapy was associated with disease recurrence (P = .023), whereas pathologic downstaging was not. Analysis of tumor-centric biomarkers showed that mutational processes (signature 5) were associated with pathologic downstaging (P = .024); however, no significant correlation for tumor subtypes, DNA damage response mutations, and other biomarkers was observed. Our results suggest that ctDNA analysis is better associated with treatment efficacy compared with other available methods.

CONCLUSION

ctDNA assessment for early risk stratification, therapy monitoring, and early relapse detection in bladder cancer is feasible and provides a basis for clinical studies that evaluate early therapeutic interventions.

Exit-Site Infection: A Comparison of Classification Systems

In general, in peritoneal dialysis (PD) practice in hospitals, Twardowski and Prowant's exit-site classification system is used, while the International Society for Peritoneal Dialysis (ISPD) exit-site scoring system is practical to use in community visits with less experienced healthcare personnel. Nevertheless, when exit-site scoring is 3 points under the ISPD exit-site score system and it falls in the category of equivocal under the Twardowski and Prowant's exit-site classification, the physician should be vigilant about the possibility of developing peritonitis, and hence, patients need to be kept under periodic monitoring.

Cephalic Arch Stenosis: Location of Stenosis in Indian Hemodialysis Patients

The cephalic vein is formed over the "anatomical snuff box" and joins the axillary vein just below the clavicular level. The definition of cephalic arch is varied. In the radiology literature, it is defined as the central perpendicular portion of the cephalic vein as it traverses the deltopectoral groove and joins the axillary vein. The possible etiologies of cephalic arch stenosis are numerous. This study aimed to identify patients with cephalic arch stenosis and to discern the domain site of stenosis. This is a retrospective case series of patients who had an arteriovenous fistula with dysfunction of access and ipsilateral upper-limb edema. The clinical features of the access dysfunction were strong pulse due to increased pressure, weak thrill due to poor proximal flow, high static pressure, or decreased dialysis efficiency. All these 25 patients underwent computed tomography (CT) angiogram. The CT angiographic findings revealed cephalic arch stenosis and stenosis in 13 patients (52%). domain IV was slightly more affected than other domains of cephalic arch.

Mitochondrial Neurogastrointestinal Encephalomyopathy: A Nonrenal Indication for Peritoneal Dialysis

Mitochondrial neurogastrointestinal encephalomyopathy is a rare autosomal recessive disorder characterized by severe muscle wasting, gastrointestinal dysmotility, leukoencephalopathy, peripheral neuropathy, and ophthalmoplegia. The pathogenesis involves the accumulation of very high concentrations of nucleosides dThd and dUrd along with depletion of nucleotide dCTP. One of the treatment measures is the removal of nucleosides dThd and dUrd by hemodialysis and peritoneal dialysis. Only a few patient reports of dialysis as a measure to remove nucleosides had been reported.

Association of Amelogenesis Imperfecta and Bartter's Syndrome

Bartter's syndrome is an autosomal recessive renal tubular disorder characterized by hypokalemia, hypochloremia, metabolic alkalosis, and hyperreninemia with normal blood pressure. Bartter's syndrome is associated with hypercalciuria and nephrocalcinosis. Amelogenesis imperfecta (AI) is a group of hereditary disorders that affect dental enamel. AI could be part of several syndromes. The enamel renal syndrome is the association of AI and nephrocalcinosis. We report two patients of AI with Bartter's syndrome.

Toxic Epidermal Necrolysis and Acute Kidney Injury due to Glyphosate Ingestion

The literature, particularly from India, is scarce on the renal effects of glyphosate poisoning. Glyphosate causes toxicity not only after its ingestion but also after dermal exposure by inhalation route and on eye exposure. We present a patient report of glyphosate consumption which resulted in toxic epidermal necrolysis – the first report after glyphosate consumption and acute kidney injury.

Renal Manifestations in Paroxysmal Nocturnal Hemoglobinuria

Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired chronic disorder characterized by a triad of clinical features - hemolytic anemia, pancytopenia, and thrombosis. Not many reports of renal involvement in PNH are available in literature. We present a case series of PNH with renal involvement. We present the data of PNH patients who attended to Departments of General Medicine and Nephrology at a government-run tertiary care institute in South India. The diagnosis of PNH in these patients during initial phase, between 1998 and 2004 was based on sucrose lysis and Ham's test. After 2004, the diagnosis was based on flow cytometry to detect CD59 (membrane inhibitor of reactive lysis), a glycoprotein, and CD55 (decay accelerating factor) in regulation of complement action. The patient data were collected from 1998 to 2014. There were 14 patients of PNH in this period. The mean age was 37 years and the range was 16–68 years. There were eight females. Acute kidney injury (AKI) was noted in six patients. Dialysis was performed in four of them. The mean serum creatinine and urea at the initiation of dialysis were 5.4 ± 0.6 and 64.1 ± 6.1 mg/dl, respectively. The median number of hemodialysis sessions done was four. Renal biopsy was done in four patients. In three patients, the urinalysis and serum chemistry were suggestive of Fanconi syndrome. In our patients, three renal manifestations of PNH were identified. They were AKI, renal vessel thrombosis, and Fanconi syndrome. Chronic renal failure was not identified.

Employment Status of Patients Receiving Maintenance Dialysis - Peritoneal and Hemodialysis: A Cross-sectional Study

The long-term dialysis therapy for end-stage renal disease takes a heavy toll of quality of life of the patient. Several factors such as fatigue and decreased physical capability, impaired social and mental functioning, contribute to this forlorn state. To meld maintenance dialysis treatment with a regular employment can be a serious test. A cross-sectional study of employment of patients on hemodialysis and peritoneal dialysis in a state government tertiary institute in South India was performed between June 2015 and December 2015. Patients who completed 3 months of regular dialysis were only included in the study. The number of patients on hemodialysis was 157 and on peritoneal dialysis was 69. The employment status before the initiation of dialysis was 60% (93 out of 155) and 63.7% (44 out of 69) in hemodialysis and peritoneal dialysis, respectively. After initiation, the loss of employment was observed in 44% (41 out of 93) in hemodialysis and 51.2% (26 out of 44) in peritoneal dialysis (P = 0.2604). Even though there was fall of absolute number of job holders in both the blue and white collar jobs, the proportion of jobholders in the white collar job holders improved. On univariate analysis, the factors which influenced the loss of employment were males, age between 50 and 60 years, number of comorbidities >2, illiteracy and blue collar versus white collar job before the initiation of dialysis. The majority of patients had the scores above 80 on Karnofsky performance scale and the majority belonged upper and middle classes than lower classes on modified Kuppuswamy's socioeconomic status scale; however, the loss of employment was also disproportionately high. There appeared a substantial difference in the attitude of the patients toward the employment. There was no difference between hemodialysis and peritoneal dialysis in the loss of employment of our patients.

Phlegmasia cerulean dolens: complication of femoral vein catheterization

There are three less frequent manifestations of acute massive venous thrombosis and obstruction of the venous drainage of an extremity. They are phlegmasia alba dolens, phlegmasia cerulean dolens (PCD), and venous gangrene. The term PCD differentiates ischemia-associated massive venous thrombosis from phlegmasia alba dolens, which describes fulminant venous thrombosis without ischemia. We present a 55-year-old hypertensive, who presented with paedal oedema and breathlessness at rest. About a month prior to this admission, she suffered dislocation of left patella. She was treated with a plaster cast and immobilization for 3 weeks. Her serum creatinine was 8.8 mg/dL. She was initiated on haemodialysis via two single-lumen catheters placed in left femoral vein. The femoral vein catheters were removed after third session of haemodialysis. On fourth day, the patient complained pain and blue discolouration of left toes. On examination, the left lower limb was swollen, discoloured, and cold with blebs up to upper one-third of left leg. The left dorsalis pedis and posterior tibial arteries were not palpable. A Doppler of veins of lower limb revealed, thrombosis of deep, and superficial venous system of left lower limb. As there was no response to anticoagulation below, knee amputation was performed.

A common variant association study reveals novel susceptibility loci for low HDL-cholesterol levels in ethnic Arabs

The genetic susceptibility to acquiring low high density lipoprotein-cholesterol (LHDLC) levels is not completely elucidated yet. In this study, we performed a common variant association study for harboring this trait in ethnic Arabs. We employed the Affymetrix high-density Axiom Genome-Wide ASI Array (Asian population) providing a coverage of 598,000 single nucleotide variations (SNPs) to genotype 5495 individuals in a two-phase study involving discovery and validation sets of experiments. The rs1800775 [1.31 (1.22-1.42); p = 3.41E-12] in the CETP gene and rs359027 [1.26 (1.16-1.36); p = 2.55E-08] in the LMCD1 gene were significantly associated with LHDLC levels. Furthermore, rs3104435 [1.26 (1.15-1.38); p = 1.19E-06] at the MATN1 locus, rs9835344 [1.16 (1.08-1.26); p = 8.75E-06] in the CNTN6 gene, rs1559997 [1.3 (1.14-1.47); p = 9.48E-06] in the SDS gene and rs1670273 [1.2 (1.1-1.31); p = 4.81E-06] in the DMN/SYNM gene exhibited suggestive association with the disorder. Seven other variants including rs1147169 in the PLCL1 gene, rs10248618 in the DNAH11, rs476155 in the GLIS3, rs7024300 in the ABCA1, intergenic rs10836699, rs11603691 in P2RX3 and rs750134 in CORO1C gene exhibited borderline protective properties. Validation and joint meta-analysis resulted in rs1800775, rs3104435 and rs359027 retaining their predisposing properties, while rs10836699 and rs11603691 showed protective properties. Our data show several predisposing variants across the genome for LHDLC levels in ethnic Arabs.

Busulfan fludarabine vs busulfan cyclophosphamide as a preparative regimen before allogeneic hematopoietic cell transplantation: systematic review and meta-analysis

We aimed to evaluate the efficacy and toxicity profile of busulfan-fludarabine (Bu-Flu) compared with busulfan-cyclophosphamide (Bu-Cy) as a preparative regimen for patients undergoing allogeneic hematopoietic cell transplantation. We performed a systematic review and meta-analysis of all comparative trials, both randomized controlled trials (RCTs) and non-randomized. Our search yielded 15 trials recruiting 1830 patients. Four trials were RCTs and 11 were either one-arm intervention trials compared with historical controls or retrospective studies. There was a lower risk for non-relapse mortality (NRM) at 100 days in patients given Bu-Flu regimen compared with those given Bu-Cy regimen (relative risk (RR) 0.56; 95% confidence interval (CI) 0.34-0.92, 8 trials); however, there were no differences in all-cause mortality at 100 days (RR 0.85; 95% CI 0.56-1.30, 9 trials) and at the end of study (RR 0.81; 95% CI 0.64-1.02, 13 trials). The risks of sinusoidal obstruction syndrome (SOS) and microbiologically documented infections were lower in patients given Bu-Flu regimen (RR 0.34; 95% CI 0.19-0.62, 8 trials and RR 0.79; 95% CI 0.64-0.97, 2 trials, respectively); however, risk for SOS was no longer lower when performing sensitivity analysis according to RCTs. Engraftment kinetics, risk of grade 3-4 mucositis, GvHD, relapse and NRM at the end of the study were all similar between the two groups. We conclude that both regimens have similar efficacy profiles, whereas toxicity is lower with the Bu-Flu regimen.

Hemorrhage from lumbar artery following percutaneous renal biopsy

We present a 58-year-old lady who underwent ultrasound-guided renal biopsy for suspected acute glomerulonephritis. Within minutes, the radiologist noticed an echogenic band around left kidney and in the muscular planes. Computerized tomography revealed focal active contrast extravasation from arcuate or interlobular artery in lower pole of left kidney and lumbar artery at third lumbar vertebra. The bleeding vessel was occluded with gelfoam.

Disseminated Trichosporon infection in a renal transplant recipient

Trichosporon species are basidiomycetous yeast-like anamorphic organisms (Basidiomycota, Hymenomycetes, Tremelloidae, Trichosporonales) that are widely distributed in nature. Trichosporon species colonize the skin and gastrointestinal tract of humans. We present a report of disseminated Trichosporon in a renal allograft recipient. Our patient satisfied the definitions of both "proven invasive trichosporonosis" and "probable pulmonary infection." Only 2 reports of disseminated Trichosporon infection in renal transplant recipients, to our knowledge, have been published.

Gloriosa superba ingestion: Hair loss and acute renal failure

Gloriosa superba is a plant that grows wild in several parts of South India. Tubers of this plant contain several alkaloids. Acute intoxication following the ingestion of G. superba results in gastrointestinal and haematological abnormalities, hepatic and renal insufficiency, cardiotoxicity and hair loss. We present a case with typical features of G superba toxicity.