Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma

Liquid biopsies including circulating tumor cells (CTCs) and cell-free DNA (cfDNA) have enabled minimally invasive characterization of many cancers, but are rarely analyzed together. Understanding the detectability and genomic concordance of CTCs and cfDNA may inform their use in guiding cancer precision medicine. Here, we report the detectability of cfDNA and CTCs in blood samples from 107 and 56 patients with multiple myeloma (MM), respectively. Using ultra-low pass whole-genome sequencing, we find both tumor fractions correlate with disease progression. Applying whole-exome sequencing (WES) to cfDNA, CTCs, and matched tumor biopsies, we find concordance in clonal somatic mutations (~99%) and copy number alterations (~81%) between liquid and tumor biopsies. Importantly, analyzing CTCs and cfDNA together enables cross-validation of mutations, uncovers mutations exclusive to either CTCs or cfDNA, and allows blood-based tumor profiling in a greater fraction of patients. Our study demonstrates the utility of analyzing both CTCs and cfDNA in MM.

Circulating tumor cells (CTCs) and cell-free DNA (cfDNA) enables characterization of a patient’s cancer. Here, the authors analyse CTCs, cfDNA, and tumor biopsies from multiple myeloma patients to show these approaches are complementary for mutation detection, together enabling a greater fraction of patient tumors to be profiled.

Abstract GS3-07: Genome-wide copy number analysis of chemotherapy-resistant metastatic triple-negative breast cancer from cell-free DNA

Introduction:

Triple-negative breast cancer (TNBC) is a poor prognosis breast cancer subset characterized by relatively few mutations but extensive copy number alterations (CNAs). Cell-free DNA (cfDNA) offers the potential to overcome infrequent tumor biopsies in metastatic TNBC (mTNBC) and interrogate the genomics of chemotherapy resistance.

Methods:

506 archival or fresh plasma samples were identified from 164 patients with mTNBC who had previously received chemotherapy. We performed low coverage whole genome sequencing to determine genome-wide copy number and estimate 'tumor fraction' of cfDNA (TFx) using our recently-developed approach, ichorCNA. In patient samples with TFx >10%, we identified regions that were significantly gained or lost using GISTIC2.0. We compared CNAs of 20 paired primary-metastatic samples and also mTNBCs from cfDNA versus primary TNBCs from TCGA and METABRIC.

Results:

We successfully obtained high quality, low coverage whole genome sequencing data for 478 (94.5%) plasma samples from 158 patients, with 1 to 14 samples per patient. TFx and copy number profiles were highly concordant with paired metastatic biopsy (n=10, range 0-7 days from biopsy to blood draw) with sensitivity of 0.86 and specificity of 0.90 and reproducible in independently-processed blood draws (TFx intraclass correlation coefficient 0.984). Median overall survival from time of first blood draw was 8 months, and TFx was highly correlated independent of primary stage, primary receptor status, age at primary diagnosis, BRCA status, and metastatic line of therapy: adjusted hazard ratio between 4th and 1st quartiles = 2.14 (95% CI 1.40-3.28; p=0.00049). 101/158 patients (63.9%) had at least one sample with TFx >10%, our threshold for high confidence CNA calls. Copy number profiles and percent genome altered were remarkably similar between mTNBCs and primary TNBCs in TCGA and METABRIC (n=433), suggesting that large-scale chromosomal events are infrequent in TNBC metastatic progression. We identified chromosomal gains that demonstrated significant enrichment in mTNBCs relative to paired primary TNBCs (n=20) and also TCGA/METABRIC, including driver genes (NOTCH2, AKT2, AKT3) and putative antibody-drug conjugate targets. Finally, we identify a novel association of gains of 18q11 and/or 19p13 with poor metastatic prognosis, independent of clinicopathologic factors and TFx.

Conclusions:

Here, we present the first large-scale genomic characterization of metastatic TNBC to our knowledge, derived exclusively from cfDNA. 'Tumor fraction' of cfDNA is an independent prognostic marker in mTNBC. Primary and metastatic TNBC have remarkably similar copy number profiles yet we identify alterations enriched and prognostic in mTNBC. Collectively, these data have potential implications in the understanding of metastasis, therapeutic resistance, and novel therapeutic targets.

Citation Format: Stover DG, Parsons HA, Ha G, Freeman S, Barry B, Guo H, Choudhury A, Gydush G, Reed S, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TA, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. Genome-wide copy number analysis of chemotherapy-resistant metastatic triple-negative breast cancer from cell-free DNA [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr GS3-07.

Fabrication of mid-infrared frequency-selective surfaces by soft lithography

We describe the fabrication of large areas (4 cm(2)) of metallic structures or aperture elements that have ~100-350-nm linewidths and act as frequency-selective surfaces. These structures are fabricated with a type of soft lithography-near-field contact-mode photolithography-that uses a thin elastomeric mask having topography on its surface and is in conformal contact with a layer of photoresist. The mask acts as an optical element to create minima in the intensity of light delivered to the photoresist. Depending on the type of photoresist used, lines of, or trenches in, photoresist are formed on the substrate by exposure, development, and lift-off. These surfaces act as bandpass or bandgap filters in the infrared.

Atrial fibrillation: a risk factor for increased mortality--an AVID registry analysis

Emerging evidence suggests that atrial fibrillation is not a benign arrhythmia. It is associated with increased risk of death. The magnitude of association is controversial and potential causes remain unknown. Patients in the registry of the Antiarrhythmics Versus Implantable Defibrillators (AVID) Trial form the basis for this report. Baseline variables, in particular the presence or absence of a history of atrial fibrillation/flutter, were examined in relation to survival. Multivariate Cox regression was used to adjust for differences in important baseline co-variables using 27 pre-selected variables. There were 3762 subjects who were followed for an average of 773+/-420 days; 1459 (39 %) qualified with ventricular fibrillation and 2303 (61 %) with ventricular tachycardia. A history of atrial fibrillation/flutter was present in 24.4 percent. There were many differences in baseline variables between those with and those without a history of atrial fibrillation/flutter. After adjustment for baseline differences, a history of atrial fibrillation/flutter remained a significant independent predictor of mortality, (relative risk=1.20; 95 % confidence intervals=1.03-1.40; p=0.020). Antiarrhythmic drug use, other than amiodarone or sotalol, was also a significant independent predictor of mortality (relative risk 1.34; 95 % confidence intervals 1.07-1.69, p=0.011. Atrial fibrillation/flutter is a significant independent risk factor for increased mortality in patients presenting with ventricular tachyarrhythmias. This risk may have been overestimated in previous studies that could not adjust for the proarrhythmic effects of antiarrhythmic drugs other than amiodarone or sotalol.

Prenatal diagnosis of ventriculocoronary fistula

BACKGROUND

Cardiac anomalies may be associated with abnormal coronary vascular connections. We report the prenatal diagnosis of ventriculocoronary fistula in three fetuses with associated cardiac anomalies.

MATERIALS AND METHODS

Fetal echocardiography was performed in three patients referred for suspected cardiac anomaly. Two-dimensional fetal echocardiography was complemented by color Doppler flow imaging and spectral Doppler in all cases.

RESULTS

A ventriculocoronary fistula was diagnosed in three patients referred at 22, 23 and 32 weeks. The first patient had hypoplastic left heart associated with transposition of the great arteries and pulmonary atresia with an intact interventricular septum. The coronary fistula arose from the transposed aorta to the left ventricle. In two patients ventriculocoronary fistula was found in association with pulmonary atresia and an intact interventricular septum. In all cases there was bidirectional flow within the fistula (diastolic blood flow towards the ventricle with reversal during ventricular systole). The pregnancy with hypoplastic left heart with transposition, and one of those with pulmonary atresia resulted in neonatal death and stillbirth, respectively. In the third instance the ventriculocoronary fistula was verified by postpartum cardiac angiography. The infant initially received a Blalock-Taussig shunt, subsequently replaced by a bidirectional Glenn shunt, and was doing well at the time of writing.

CONCLUSION

A ventriculocoronary fistula can be identified prenatally by color and spectral Doppler. This anomaly should be sought in fetuses with outflow tract obstructive cardiac lesions and an intact interventricular septum. Prenatal diagnosis allows early angiography postnatally. Delineation of coronary vascular regions may therefore facilitate preoperative planning.

Clinical evaluation comparing AxSYM CA 15-3, IMx CA 15-3 and Truquant BRTM RIA

A retrospective clinical study was conducted to compare results obtained by AxSYM(R) CA 15-3(TM), IMx(R) CA 15-3 and Truquant(R) BRTM RIA using surplus serum specimens from healthy volunteers and patients with benign and malignant diseases. Linear regression analysis of AxSYM and IMx CA 15-3 versus Truquant BR RIA for specimens with results 0-250 U/ml gave correlation coefficients of 0. 888 and 0.910 and slopes of 0.67 and 0.69, respectively. For specimens with results 0-2,000 U/ml, slopes were 0.95 and 0.91, respectively. Receiver operator characteristic analyses, based on results from healthy females plus nonmalignant disease patients versus breast cancer patients, for all three assays gave essentially equivalent areas under the curves. Concordance between AxSYM or IMx CA 15-3 and Truquant BR RIA was greater than 92%. Serial dilution of seven serum specimens yielded linear regression correlation coefficients ranging from 0.997 to 1.000 for AxSYM and IMx CA 15-3, and from 0.962 to 0.998 for Truquant BR RIA. The average percent CVs of the calculated assay values for the 7 specimens were 4.9, 2.7 and 18.1 for AxSYM CA 15-3, IMx CA 15-3 and Truquant BR RIA, respectively. Average percent recoveries ranged from 96.2 to 110.7 for AxSYM and IMx CA 15-3, and 81.8 to 93.3 for Truquant BR RIA. Although assay values differ between the two methodologies, AxSYM CA 15-3, IMx CA 15-3 and Truquant BR RIA showed comparable trending results for the 24 breast cancer patients evaluated for serial monitoring.

Recurrent pain after hysterectomy and bilateral salpingo-oophorectomy for endometriosis: evaluation of laparoscopic excision of residual endometriosis

Endometriosis can represent with a variety of symptoms including pelvic pain, dyspareunia and pain with defaecation, up to several years after hysterectomy and bilateral salpingo-oophorectomy. This may occur when all endometriotic tissue is not excised at the time of the initial procedure. Although excision of endometriosis at this time would be preferable, we have found laparoscopic excision of residual endometriosis to be effective in relieving endometriosis associated pain.

Aortic stenosis and patent ductus arteriosus: pressure gradients pre- and posttranscatheter ductal occlusion

Three patients with patent ductus arteriosus and moderate aortic stenosis had a marked reduction in aortic valve gradient following transcatheter ductal occlusion. The hemodynamic effects of an aortopulmonary shunt on the severity of left ventricular outflow obstruction and the implications on intervention are discussed.

Comparison of clinical characteristics and frequency of implantable defibrillator use between randomized patients in the Antiarrhythmics Vs Implantable Defibrillators (AVID) trial and nonrandomized registry patients

In the Antiarrhythmics Vs Implantable Defibrillators (AVID) trial, all patients who meet the study entry criteria are followed in a registry. During the period between June 1993 and June 1995, of 1,117 patients who were enrolled in the registry and met the study entry criteria, 476 were randomized to receive either implantable cardioverter-defibrillators (ICDs) or drug therapy (amiodarone or sotalol), and 641 patients were not randomized for a variety of reasons including: patient refusal (42%); physician refusal (43%); concerns about ability to maintain follow-up over several years (10%), and others (6%). There were no significant differences between the 476 randomized and 641 nonrandomized patients with regard to clinical characteristics, left ventricular function, history of congestive heart failure, medical history, and previous cardiac procedures performed before the index event, except that randomized patients were slightly older (65 vs 62 years) and had a slightly higher prevalence of coronary artery disease and previous myocardial infarction. The index event and location of the index event were not significantly different between the 2 groups. Although 14% of registry patients received neither ICD nor antiarrhythmic drug therapy, ICDs were no more frequently used in the registry patient than antiarrhythmic drugs (45% for ICD vs 42% for drugs). Thus, randomized AVID patients have very similar clinical characteristics, cardiac history, and presenting arrhythmias as to nonrandomized eligible patients. Therefore, the results of the AVID trial may be generalized for all patients with AVID-eligible arrhythmias.

Implantation of balloon-expandable stents for coarctation of the aorta: implantation data and short-term results

We report the immediate results and the short-term follow-up in a group of selected patients with coarctation of the aorta who underwent endovascular stent implantation. Balloon-expandable stents were implanted in 6 patients (mean age 19.8 +/- 5.1 years) with coarctation of the aorta (4 recurrent and 2 native) who underwent a total of 7 procedures (6 implantation and 1 further expansion). The systolic peak pressure gradient was decreased from 36.7 +/- 16.9 to 13.3 +/- 23.2 mm Hg (P < 0.005). There was a 66% increase in the mean coarctation diameter from 9.3 +/- 1.7 to 15.6 +/- 3.1 mm (P = 0.001) with the ratio of the coarctation to descending aorta diameter, measured at the level of the diaphragm, increasing from 0.49 +/- 0.1 to 0.81 +/- 0.2 (P < 0.005). The dilatation was successful in expanding the stent to an acceptable diameter in 5 of 6 patients. One patient underwent successful further expansion of a stent implanted 22 months previously. There were no immediate complications during balloon expansion and stent implantation. One patient suffered a femoral arterial bleed requiring surgical repair. There was one unrelated death. All patients were hypertensive (systolic blood pressure > 140 mm Hg) prior to stent implantation. At mean follow-up of 8 months, 3 patients are normotensive. There was no recurrence of coarctation, aortic dissection, or aneurysm formation in the patients in whom stent implantation was successful. These findings indicate that balloon-expandable stent implantation for coarctation of the aorta in selected patients is a safe and effective alternative approach for relieving the obstruction with a low complication rate and no recoarctation at short-term follow-up.

Implantation of balloon-expandable stents for coarctation of the aorta: implantation data and short-term results

We report the immediate results and the short-term follow-up in a group of selected patients with coarctation of the aorta who underwent endovascular stent implantation. Balloon-expandable stents were implanted in 6 patients (mean age 19.8 +/- 5.1 years) with coarctation of the aorta (4 recurrent and 2 native) who underwent a total of 7 procedures (6 implantation and 1 further expansion). The systolic peak pressure gradient was decreased from 36.7 +/- 16.9 to 13.3 +/- 23.2 mm Hg (P < 0.005). There was a 66% increase in the mean coarctation diameter from 9.3 +/- 1.7 to 15.6 +/- 3.1 mm (P = 0.001) with the ratio of the coarctation to descending aorta diameter, measured at the level of the diaphragm, increasing from 0.49 +/- 0.1 to 0.81 +/- 0.2 (P < 0.005). The dilatation was successful in expanding the stent to an acceptable diameter in 5 of 6 patients. One patient underwent successful further expansion of a stent implanted 22 months previously. There were no immediate complications during balloon expansion and stent implantation. One patient suffered a femoral arterial bleed requiring surgical repair. There was one unrelated death. All patients were hypertensive (systolic blood pressure > 140 mm Hg) prior to stent implantation. At mean follow-up of 8 months, 3 patients are normotensive. There was no recurrence of coarctation, aortic dissection, or aneurysm formation in the patients in whom stent implantation was successful. These findings indicate that balloon-expandable stent implantation for coarctation of the aorta in selected patients is a safe and effective alternative approach for relieving the obstruction with a low complication rate and no recoarctation at short-term follow-up.

Extracorporeal life support of neonates with congenital cardiac defects: techniques used during cardiac catheterization and surgery

Neonatal patients with congenital cardiac defects require proper diagnosis often by cardiac catheterization before surgical repair. In our institution, patients whose echocardiograms reveal surgically correctable lesions, but who are severely decompensated, have been placed on Extracorporeal Life Support (ECLS) prior to catheterization or surgery. Subsequent management of ECLS and cardiopulmonary bypass (CPB) are dictated by the surgical procedure. Hypothermia can be utilized while on ECLS to facilitate low-flow CPB, or circulatory arrest. Total extracorporeal circulation may be performed with the ECLS circuit, or the patient may be transferred to a conventional CPB circuit during the procedure. If required, post surgical ECLS can be facilitated through prior cannulation. We have found pre-operative institution of ECLS, in the neonate with severe congenital cardiac defects, provides immediate control of hemodynamic and respiratory problems, lowers the risk of cardiac catheterization, and reduces the usage of blood products during surgery.

Reversibility of hypotension and shock by atrial or atrioventricular sequential pacing in patients with right ventricular infarction

Hypotension and shock associated with heart block and other forms of atrioventricular (AV) dissociation frequently accompany right ventricular infarction ( RVI ). Such patients do not invariably improve with ventricular pacing. We evaluated the relative effects of AV dissociated rhythms (ventricular pacing or nodal rhythm) and AV synchronous rhythms (atrial pacing, AV sequential pacing, or return to normal sinus rhythm) in seven patients with RVI complicated by AV dissociation, who had hypotension or shock. Hemodynamic monitoring demonstrated the characteristic features of RVI in all patients. Restoration of AV synchrony resulted in a highly significant (p less than or equal to 0.001) increase in systolic blood pressure (88.0 +/- 16.5 mm Hg to 133.0 +/- 21.8 mm Hg), cardiac output (3.8 +/- 0.9 L/min to 5.7 +/- 0.9 L/min), and stroke volume (40.5 +/- 6.9 cc to 61.0 +/- 10.0 cc). We conclude that restoration of normal AV synchrony has a marked effect on stroke volume in this setting and that atrial or AV pacing can reverse hypotension and shock in RVI complicated by AV dissociation.

Superior vena cava syndrome. Its association with indwelling balloon-tipped pulmonary artery catheters

The placement of flow-directed pulmonary artery catheters has become a routine procedure in hospitals throughout the country. There have been scattered reports of complications associated with their placement, but in general, if it is done under proper conditions, it is associated with low morbidity and mortality. Recently, there have been questions raised regarding the thrombogenicity of these catheters. We report three cases of superior vena cava syndrome associated with the use of indwelling pulmonary artery catheters that we have encountered and a review of experience of others.

Clinical pharmacokinetics and efficacy of amiodarone for refractory tachyarrhythmias

Using a high-pressure liquid chromatographic assay, we measured serum amiodarone concentrations serially in 122 patients treated with amiodarone for 1.5-53 months (mean 9.3 months) for control of refractory symptomatic atrial or symptomatic and life-threatening ventricular tachyarrhythmias. The atrial tachyarrhythmias were successfully controlled in 45 of 54 patients (83%) during a mean follow-up of 10.0 months. In the ventricular tachyarrhythmia group, which included 22 survivors of sudden cardiac death, 38 of 50 patients (76%) responded to amiodarone during a mean follow-up of 10.9 months. Although the mean serum amiodarone concentration did not differ between responders and nonresponders, eight responders relapsed when their serum concentration fell below 1.0 mg/l. Side effects resulted in withdrawal of amiodarone in only 10 of 122 patients (9%) despite a 30% overall incidence of side effects. Central nervous system and gastrointestinal side effects became more frequent with serum concentrations greater than 2.5 mg/l, although only central nervous system side effects achieved statistical significance. Absorption and disposition kinetics of a single oral 800-mg dose of amiodarone were studied in eight patients. Serum values were measured for 24 hours in five patients during maintenance therapy, and elimination kinetics after long-term therapy were evaluated in three patients. The tissue concentration of amiodarone was determined in two patients who died during long-term amiodarone therapy and an attempt was made in 14 patients to correlate serum concentrations with daily dosages during maintenance therapy. The pharmacokinetics of oral amiodarone support the practice of using high loading dosages until arrhythmia suppression or apparent steady state is achieved (usually 2-4 weeks), followed by low-dose maintenance therapy (200-600 mg once a day) for treatment of symptomatic atrial and ventricular tachyarrhythmias.