Abstract 4284: Enhancing subclonal reconstruction algorithm for resolving complex tumor phylogenies from multi-sample tumor DNA sequencing

Cancer is characterized by the ongoing accumulation of somatic mutations, providing selective advantages that may lead to dysregulated cellular proliferation. While the cancer genome at diagnosis has been extensively studied, many cancer types still lack strong prognostic biomarkers. The continuous acquisition and selection for driver mutations in a population of cancer cells acts as a Darwinian process, resulting in clonal expansions of progressively more aberrant and fit phenotypes. Reconstructing tumor evolution allows us to understand key events that drive cancer progression and patterns of mutation co-occurrence within clones. These evolutionary features guide our understanding of fundamental mechanisms that lead to disease lethality. Inferring tumor evolution from DNA sequencing data is becoming part of routine analysis in cancer research. As sequencing costs drop, sequencing multiple tumor samples from a patient becomes routine. These multiple samples can represent different spatial regions of a tumor, longitudinal samples from a single region or a combination of both. This provides an opportunity to study tumor evolution in much greater detail and accuracy than was previously feasible through single-sample datasets. The most widely used methods to reconstruct the subclonal evolution of a tumor utilize stochastic-search algorithms. These approaches iterate through a parameter space to select phylogenetic solutions that maximize the likelihood of observed sequencing data. They are optimized for low complexity cases, where the size and number or subclones are relatively limited. As tumor subclonal structure increases in complexity, the parameter space grows exponentially, and stochastic-search algorithms become computationally intractable. For instance, recent benchmarking studies have revealed that many methods fail to reconstruct clone trees for data with as few as ten subclones. To circumvent current computational limitations, we developed a deterministic algorithm for subclonal reconstruction that leverages fundamental principles of cancer biology to encode heuristics that reduce the solution space to biologically plausible phylogenies. When applied to samples (4-36 tumors; median 16) from 12 patients with metastatic breast cancer, our method reduced the average runtime ten-fold. We were able to delineate the evolutionary history of up to 57 distinct subclones per patient, which is infeasible with most current methods. Benchmarking using methods developed for the SMCHet DREAM challenge on real and simulated datasets further quantifies the accuracy, resolution, and scalability. We have thus presented a novel method for rapid and optimized reconstruction of tumor evolutionary histories.

Citation Format: Helena Winata, Daniel Knight, Juber A. Patel, Nicholas K. Wang, Pier Selenica, Stefan E. Eng, Caroline Kostrzewa, Jaron Arbet, Yingjie Zhu, Ronglai Shen, Jorge Reis-Filho, Pedram Razafi, Paul C. Boutros. Enhancing subclonal reconstruction algorithm for resolving complex tumor phylogenies from multi-sample tumor DNA sequencing. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4284.

Development of High-Throughput Clinical Testing of RPGR ORF15 Using a Large Inherited Retinal Dystrophy Cohort

Purpose

Mutations in the ORF15 region of RPGR account for approximately half of all X-linked retinitis pigmentosa cases. However, a robust high-throughput method for the detection of ORF15 mutations has yet to be validated. We set out to develop the first clinically validated next-generation sequencing (NGS) method for the detection of mutations in this difficult-to-sequence region, including test accuracy and coverage data.

Methods

As part of a blind-test, 145 research samples, previously tested by Sanger sequencing, and 81 clinical samples were evaluated using NGS of long-range PCR products fragmented with Illumina's Nextera library preparation kit (method 1), or with Centrillion's OneTube technology, supplemented with duplication analysis using an ORF15-specific in-silico array (method 2). DNA fragments were analyzed using Agilent's DNA 1000 assay, and sequencing was done on Illumina's MiSeq 2×150 or HiSeq2500 2×100. NextGENe by SoftGenetics was used for data analysis and variant calling.

Results

The Nextera library preparation method produced 24 cases of discordance due to (in order of decreasing occurrence) false-negatives, incorrectly called variants, and a false-positive. Subsequent use of a new, OneTube NGS library preparation method, supplemented with duplication analyses, resolved discordance between Sanger and NGS data in all cases. This improvement in variant detection accuracy was largely attributed to improvement in random fragmentation offered by the enzymatic OneTube method, resulting in more complete coverage of the highly repetitive ORF15 region. Minimum coverage was roughly 320 reads for Nextera and 6800 reads for OneTube (normalized for total read counts).

Conclusions

This paper documents the first clinically validated NGS method for reliable, high-throughput sequencing of RPGR ORF15. Sensitivity and specificity of the new method were 100%, with the caveat of unclear zygosity calling for one large duplication case. These findings demonstrate a reliable and practical implementation for NGS-based diagnosis of RPGR ORF15 mutations. They also provide the foundation for targeted, high-coverage sequencing of any other repetitive regions within the genome.

Cardiotoxicity in imipramine intoxication: report of one case

Imipramine is the most commonly prescribed tricyclic antidepressant of acute life threatening self-poisoning. We report a 15-month-old boy of accidental poisoning with imipramine, who developed generalized tonic-clonic convulsions and drug-related cardiac conduction abnormalities with PR prolongation, QRS widening, and QTc lengthening. The patient's imipramine level was 1389 ng/ml. The rapid resolution of intraventricular conduction delay and normalization of the QRS-T complexes after gastric lavage, installation of activated charcoal and alkalinization of the blood strongly implicates imipramine intoxication in the etiology of the cardiotoxicity. The patient made a full recovery without neurological sequelae.

Antioxidants may mitigate the deterioration of coronary arteritis in patients with Kawasaki disease unresponsive to high-dose intravenous gamma-globulin

During the early stages of Kawasaki disease, a marked increase in oxygen-free-radicals (OFRs), which are produced by activated polymorphonuclear cells, may induce coronary arteritis. Early use of high-dose intravenous gamma-globulin (IVIG) and aspirin effectively blocked this deteriorating course of coronary arteritis; however, late use of IVIG, even using a high-dose schedule, did not achieve the same efficacy. The causes and reactions to the scenario of IVIG refractoriness have rarely been mentioned in the literature. We present an 11-month-old male infant with Kawasaki disease and deteriorating coronary arteritis owing to late use of IVIG who showed dramatic responsiveness to the addition of alpha-tocopherol and ascorbic acid. We also discuss the possible mechanism.

Spontaneous closure of ventricular septal defects in the first year of life

BACKGROUND AND PURPOSE

The recent increase in the prevalence of ventricular septal defect (VSD) has been ascribed to the improved detection of small defects with echocardiography and the wider use of screening. The aim of this study was to determine the prevalence and timing of spontaneous closure of specific types of VSD in neonates using echocardiographic screening and follow-up.

METHODS

Two-dimensional color Doppler echocardiography was performed in 3,472 clinically normal full-term neonates born at Cathay General Hospital to detect isolated VSD. The relative prevalence of muscular versus perimembranous defects and their outcome in the first year of life were evaluated.

RESULTS

VSD was found in 74 neonates (34 male, 40 female), resulting in a prevalence of 21.3/1,000 live births. There were 48 muscular, 25 perimembranous, and one subpulmonic defects. Of the 74 patients, 11 were lost to follow-up. Within the observation period of 12 months, spontaneous closure occurred in 40 patients in the muscular group and in six patients in the perimembranous group. The overall rate of spontaneous closure was 73% by the end of the first year. Only five patients with perimembranous defects received digoxin therapy.

CONCLUSIONS

The prevalence of VSD in this series of neonates was 21.3/1,000 live births. The most common location of VSD in the neonatal period was in the region of the muscular septum. Muscular defects were more likely to close spontaneously than perimembranous defects. Most muscular defects underwent spontaneous closure during the 12-month follow-up period.

Central venous catheter-induced atrial ectopic tachycardia with reverse alternating Wenckebach periods

A centrally inserted venous catheter may cause atrial ectopic tachycardia. The association of atrial ectopic tachycardia with spontaneous reverse alternating Wenckebach periodicity has rarely been reported. We describe a 4-year-old boy with tetralogy of Fallot who developed atrial ectopic tachycardia with reverse alternating Wenckebach periods postoperatively after central venous catheter placement. All such episodes emerged from a 3:2 atrioventricular block, followed by runs of 2:1 atrioventricular block with progressive shortening of the conducted PR intervals. Normal sinus rhythm returned after the catheter was withdrawn to the superior vena cava. Reverse alternating Wenckebach periodicity may be a tachycardia-dependent physiologic phenomenon.

Multi-undulant T-U-wave, sinus bradycardia and long QT syndrome: a possible phenotype of mutant genes controlling the inward potassium rectifiers

Inward rectifying potassium currents (Ikr and Iks) during phase 3 repolarization of the myocyte from the beginning to the end of repolarization of the myocardial syncytium will inscribe a T-U-wave on the surface electrocardiogram (ECG). Type two congenital long QT syndrome (LQT2) is a phenotype of human ether-a-go-go-related gene (HERG) mutation on the chromosome 7q 35-36. Type one congenital long QT syndrome (LQT1) is a phenotype of KvLQT1 mutation on the chromosome 11p15.5. Both LQT1 and LQT2 relate with inward rectifying potassium currents and is repolarization related, therefore, it is speculate that patients of LQT1 and LQT2 may have an abnormal T-U-wave on their surface ECG. To two probands of congenital LQT, 8 patients of structural heart disease treated by open heart surgery, 13 patients of structural heart disease without open-heart surgery, and 10 patients of normal controls, 24 hour-Holter monitoring was performed from July to December 1996. Their corrected QT interval (QTc) as well as the RR interval of every heart beat was calculated by a computer. The results showed that all 33 patients exhibited beat-by-beat fluctuation of their QTc and RR daily. The RR intervals of these two probands of congenital LQT were somewhile more than 1200 ms during circadian waking time, while 31 cases without LQT showed their RR prolongation only during the circadian sleeping time. A multi-undulant T-U-wave, or a beat-to-beat changing of vectors or amplitudes of their T-U-wave observed in these two probands of congenital LQT, were not observable in those 31 patients without congenital LQT. Therefore, we concluded that multi-undulant T-U-wave, sinus bradycardia and a longer QTc was a phenotype of the mutated genes which control the inward rectifying potassium currents during phase 3 repolarization.

Prognostic value of color Doppler echocardiographic findings in premature newborns with patent ductus arteriosus

This study intended to evaluate the relationship between the prognosis for premature newborns (PM) with patient ductus arteriosus (PDA) and their Doppler echocardiographic findings. From January 1989 to December 1995, of 369 premature newborns in their first postnatal week, 196 underwent ductal evaluations echocardiographically: 47 of these 196 cases were found to have PDA. Each echocardiogram had complete data for cardiac output, ejection fraction, the left atrial-to-the-aortic ratio (LA/AO), the systolic time interval of the right ventricle (RVSTI), the transvalvular pressure gradient from tricuspid regurgitation (TGTR) and ductal Doppler color flow maps. These 47 premature newborns with PDA were grouped into (A) "asymptomatic" patients whose ductus closed spontaneously within a one-year follow-up (15 subjects), (B) "symptomatic" patients whose ductus were closed by pharmacological or surgical managements (20 subjects), and (C) "complicated" patients whose ductus caused mortality of the host (12 subjects). The remaining 149 premature newborns with a closed ductus (CD) served as controls. The RVSTI in these 47 premature newborns with PDA was found to be significantly higher than those of 149 CD (0.26 +/- 0.12 vs. 0.18 +/- 0.06, p < 0.005), and denoting that PM-PDA had a higher mean pulmonary arterial pressure. The TGTR of these 47 premature newborns with PDA was also higher than these of the 149 CD controls (30.50 +/- 11.85 mmHg vs. 20.54 +/- 6.88 mmHg, p < 0.005), denoting that PM-PDA had a higher pulmonary arterial systolic pressures. Gestational age of group C neonates was younger than group A (29.46 +/- 3.41 weeks vs. 32.80 +/- 2.78 weeks, P < 0.01). The birth weight of Group C neonates was lower than that of Group A (1366.17 +/- 684.28 gm vs. 2061.67 +/- 751.77 gm. p < 0.01), therefore, extreme prematurity and small-for-gestational-age could have increased the mortality of PM-PDA. Doppler color flow maps of group C showed a wider ductal patency, less ductal waist-narrowing, more vehement red-color forward flow and less midstream mosaicism. It was concluded that patient with extreme prematurity, with very-low-birth-weight or wider patent ductus, higher pulmonary hypertension, less midstream mosaicism, or less ductal waist-narrowing would have a poorer prognosis.

Effect of continuous positive airway pressure on cardiac output in neonates

To determine the cardiac output change in neonates who were under nasal continuous positive airway pressure (CPAP) therapy, eleven newborn neonates, who were admitted to our neonatal intensive care unit with respiratory diseases, were enrolled in the study. Cardiac output was measured by pulsed Doppler echocardiogram at various pressures of 0, 2, 4, 6, 8, and 10 cm H2O and revealed 301 +/- 47, 300 +/- 49, 289 +/- 55, 275 +/- 64, 269 +/- 59 and 242 +/- 50 ml/min/kg, respectively. Cardiac output depressed significantly between 0 cm H2O and 8 cm H2O (P = 0.025), and between 0 cm H2O and 10 cm H2O (P = 0.004). We conclude that cardiac output may be depressed in neonates who are under high levels of nasal CPAP therapy, and suggest that high levels of nasal CPAP therapy must be used with caution, especially when the therapy is applied to the low birth weight neonates.

An echocardiographic study on asymptomatic multiple interatrial septal defects in newborns

In a prospective study on the integrity of the interatrial septum in the neonates, multiple interatrial septal defects or openings with shunting were discovered in nine neonates by means of the color flow mapping technique used in their first week of life among 130 Chinese neonates. Eight of the nine neonates had two openings each, and the remaining one had four openings. Thus a total of 20 openings were found in the 9 neonates. Openings located between the tip of the flap valve and the superior limbus of the foramen ovale were classified as "location A openings" (valve-like openings). Those located at the flap valve itself were classified as "location B openings" (fenestrations). Each of the 9 neonates had one opening at location A, eight of them had another opening at location B; one had three openings at location B. Six of the nine neonates were followed up at age of one month, three months and six months by means of color-flow mapping, with a total of six openings at location A and eight openings at location B. Four out of the six openings of location A and seven out of the eight openings at location B closed spontaneously before the age of six months. In conclusion, seven percent (9/130) of these Chinese neonates have multiple interatrial openings. The openings tend to close spontaneously, regardless of their locations.

Reevaluation of streptococcal infection in the pathogenesis of Kawasaki disease

Twenty-five sera from forty-nine children with Kawasaki disease (KD) in the convalescent stage, and 191 sera from controls did not disclose a higher anti-streptolysin O titer; 23 bacterial cultures from the throat swab of KD patients during the acute stage did not show a higher rate of streptococcal isolation. It was therefore concluded that there was no relation between the genesis of KD and direct immediate streptococcal infection.

Cerebral blood flow velocity in newborn infants with asphyxia

A pulsed-Doppler real-time technique was used to assess the anterior cerebral artery (ACA) flow velocity in 30 asphyxiated infants during the first 5 days after birth. Thirty healthy term infants were also studied as controls. Peak systolic flow velocity (PSFV), end diastolic flow velocity (EDFV), mean flow velocity (MFV), and pulsatility index (PI) were measured. Mean PI values of the ACA of the asphyxiated and control groups were 0.63 +/- 0.05 vs 0.71 +/- 0.04 (p less than 0.001) on the first day; 0.64 +/- 0.03 vs 0.70 +/- 0.05 (p less than 0.001) on the third day and 0.69 +/- 0.04 vs 0.70 +/- 0.04 (p greater than 0.05) on the fifth day of life. The asphyxiated group also had significantly higher EDFV and MFV than those of control group until the 5th day of life. The low PI values of asphyxiated infants were mainly due to an increase in EDFV. These results suggest that the cerebrovascular resistance of asphyxiated infants, as reflected by the PI, is low during the first 3 days of life, indicating an increase in cerebral blood flow. With this technique, we can repeatedly and safely evaluate the cerebral hemodynamic changes in asphyxiated newborn infants.

Echocardiographic changes following balloon valvuloplasty in valvular pulmonic and aortic stenosis

Nineteen patients with pulmonary valvular stenosis and two with aortic valvular stenosis, aged 20 days to 12 years, were studied before and after balloon dilatation valvuloplasty (BDV) by M-mode, 2-D, pulsed wave (PW) and continuous wave (CW) Doppler, and color flow mapping echocardiography. In those with pulmonary stenosis, a dome-shaped valve was found in 16(84%) of 19 cases before BDV, and the valve remained dome shaped only in 4(27%) of 15 after procedure (P less than 0.001). Restricted valve motion which was noted in 18(95%) of 19 before BDV, persisted only in 2(13%) of 15 after procedure (P less than 0.001). Thickening of the pulmonic valve and poststenotic dilatation of the main pulmonary artery stayed almost unchanged. The pressure gradient across the pulmonic valve measured by cardiac catheterization and CW Doppler agreed well (r = 0.862). Echocardiographic evidence of pulmonary regurgitation was detected in 1(25%) of 4 patients before, and 7(50%) of 14 after BDV. In two patients with aortic stenosis, the echocaardiograms showed the valve was thickened and dome-shaped. Following BDV, echocardiographic evidence of mild aortic regurgitation was observed only in one patient who had had such a regurgitationn before BDV. The diameter of the valve annulus measured on 2-D echo and angiocardiograms correlated well (r = 0.912), and it stayed unchanged following BDV. It is concluded that 2-D and Doppler echocardiographic examinations proved to be useful in the measurement of valve annulus, delineation of stenotic semilunar valves and monitoring of the efficacy of BDV.

Pulmonary venous obstruction and atrioventricular canal anomalies: role of cor triatriatum and double outlet right atrium

Two-dimensional echocardiographic findings and surgical repair in three infants with atrioventricular (AV) canal and pulmonary venous obstruction are described. The AV canal was complicated by cor triatriatum in two patients and by double outlet right atrium in the other. In patients with AV canal, anatomic obstruction of pulmonary venous return should be excluded by detailed cardiac ultrasound examination.