Comparison of real-world treatment patterns in chronic lymphocytic leukemia management before and after availability of ibrutinib in the province of British Columbia, Canada

We performed a retrospective study comparing treatment patterns and overall survival (OS) in chronic lymphocytic leukemia (CLL) patients with the advent of ibrutinib to provide current real-world data.

METHODS

Using a provincial population-based database, we analyzed CLL patients who received upfront treatment in British Columbia before ibrutinib availability (1984-2014), during ibrutinib access for: relapse only (2014-2015) and for upfront treatment of patients (with 17p deletion or unfit for chemotherapy) (2015-2016). Analysis included up to third-line treatment.

RESULTS

Of 1729 patients meeting inclusion criteria (median age, 66 years; 1466, period 1; 140, period 2; 123, period 3), FR was the most common first-line therapy (35.8 %, 54.3 % and 40.7 %, periods 1-3, respectively) and 18.7 % received ibrutinib upfront in period 3. The most common therapies in relapse were chemoimmunotherapy (36.1 % and 55.6 %, periods 1 and 2, second-line; 29.2 %, period 1, third-line) and ibrutinib (69.8 %, period 3, second-line; 46.4 % and 70.3 %, periods 2 and 3, third-line). OS improved for patients treated in periods 2-3 over period 1 (median OS not reached vs. 11.9 years, p < 0.001; no difference in OS for periods 2-3, p = 0.385).

CONCLUSION

Ibrutinib has replaced chemoimmunotherapy as the preferred therapy in relapse. Overall survival has improved over time with access to ibrutinib.

Fluzone® Intradermal Quadrivalent Influenza Vaccine

INTRODUCTION

An intradermal version of Fluzone® split-virion inactivated trivalent influenza vaccine, containing 9 µg hemagglutinin per strain of A/H1N1, A/H3N2, and one B lineage virus (Fluzone Intradermal, Sanofi Pasteur), became available in the US during the 2011-2012 influenza season for adults 18-64 years of age. In advance of the 2015-2016 season, Fluzone Intradermal was replaced with Fluzone Intradermal Quadrivalent vaccine, which contains 9 µg hemagglutinin per strain of the two A-strain viruses and both B-strain lineage viruses (Victoria and Yamagata).

AREAS COVERED

This literature review summarizes the history and mechanism of intradermal vaccination, discusses the clinical trial results supporting the immunogenicity and safety of Fluzone Intradermal Quadrivalent vaccine, and describes the unique microinjection system used to deliver Fluzone Intradermal Quadrivalent. Expert commentary: Fluzone Intradermal Quadrivalent may boost confidence in influenza vaccination with the addition of a second B-lineage strain. By using an innovative microinjection system, the vaccine is also designed to address some of the logistic challenges faced by healthcare providers administering immunizations.

Catastrophic antiphospholipid syndrome presenting with pulmonary hemorrhage: case report

This is a case report of catastrophic antiphospholipid syndrome (APLS) involving the rare manifestation of pulmonary hemorrhage. This rare variant of APLS is frequently life threatening despite medical therapy. The pathogenesis of pulmonary hemorrhage in catastrophic APLS remains incompletely understood. The optimal approach to managing pulmonary hemorrhage in the setting of catastrophic APLS is still unclear, however this case report demonstrates the success of combination therapy with anticoagulation, corticosteroids and plasma exchange.

Abstract 4913: Highly complex oligonucleotide libraries for use in high-resolution RNA and RNA/DNA fluorescence in situ hybridization in various sample types

Fluorescence in situ Hybridization (FISH) is a powerful technique for determining the localization specific nucleic acid sequences within individual cells. Previously, the use of FISH has often been dependent upon access to cloned template DNA for the generation of probes, which can be difficult if clones for specific regions are unavailable, or if the genomic region of interest contains repetitive and/or other problematic sequences. We have developed the ability to chemically synthesize DNA in massively parallel reactions, which we have used to produce libraries of oligonucleotides up to 200 bases in length that can be utilized for the generation of FISH probes. The sequences of the oligonucleotides in these libraries are selected in silico using empirically determined criteria so as to avoid repetitive elements or regions homologous to other non-targeted loci. We have found that these oligonucleotide library-derived FISH probes can detect human genomic regions as small as 1.8 kb and as large as whole chromosomes in both metaphase and interphase cells, using the same simple assay protocol. Because of the inherent flexibility in our probe design methods, we can readily visualize regions rich in repeats and/or GC content. We have also used these oligonucleotide library-derived FISH probes to detect the localization of a variety of both coding and non-coding RNAs in fixed tissue culture cells and formalin-fixed paraffin-embedded tissue sections, using both conventional fluorescence and structured illumination microscopy. Simultaneous hybridization of FISH probes labeled with different fluorophores enables visualization of multiple sequences at once. Using probes designed specifically to transcribed vs. non-transcribed regions has enabled the simultaneously detect DNA and RNA from the same locus, or from two different loci, in the same FISH assay. The ability to generate high performance FISH probes using chemically synthesized oligo libraries that can simultaneously detect DNA and RNA yields a valuable tool for studies of how localization of specific nucleic acids impacts biological function.

Citation Format: Robert A. Ach, Mistuni Ghosh, Peter Tsang, Alicia Scheffer-Wong, Laurakay Bruhn, Alice Yamada. Highly complex oligonucleotide libraries for use in high-resolution RNA and RNA/DNA fluorescence in situ hybridization in various sample types. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4913. doi:10.1158/1538-7445.AM2015-4913

Coherence experiments in single-pixel digital holography

In optical scanning holography (OSH), the coherence properties of the acquired holograms depend on the single-pixel size, i.e., the active area of the photodetector. For the first time, to the best of our knowledge, we have demonstrated coherent, partial coherent, and incoherent three-dimensional (3D) imaging by experiment in such a single-pixel digital holographic recording system. We have found, for the incoherent mode of OSH, in which the detector of the largest active area is applied, the 3D location of a diffusely reflecting object can be successfully retrieved without speckle noise. For the partial coherent mode employing a smaller pixel size of the detector, significant speckles and randomly distributed bright spots appear among the reconstructed images. For the coherent mode of OSH when the size of the pixel is vanishingly small, the bright spots disappear. However, the speckle remains and the signal-to-noise ratio is low.

Abstract 1513: Use of complex oligonucleotide libraries for concurrent high-resolution fluorescence imaging of both DNA and RNA in various sample types

Fluorescence in situ Hybridization (FISH) is a powerful technique for determining the localization specific nucleic acid sequences within individual cells. Previously, the use of FISH has often been dependent upon access to cloned template DNA for the generation of probes, which can be difficult if clones for specific regions are unavailable, or if the genomic region of interest contains repetitive and/or other problematic sequences. We have developed the ability to chemically synthesize DNA in massively parallel reactions, which we have used to produce libraries of oligonucleotides up to 200 bases in length that can be utilized for the generation of FISH probes. The sequences of the oligonucleotides in these libraries are selected in silico using empirically determined criteria so as to avoid repetitive elements or regions homologous to other non-targeted loci. We have found that these oligonucleotide library-derived FISH probes can detect human genomic regions as small as 1.8 kb and as large as whole chromosomes in both metaphase and interphase cells, using the same simple assay protocol. Because of the inherent flexibility in our probe design methods, we can readily visualize regions rich in repeats and/or GC content. We have also used these oligonucleotide library-derived FISH probes to detect the localization of a variety of both coding and non-coding RNAs in fixed tissue culture cells and formalin-fixed paraffin-embedded tissue sections, using both conventional fluorescence and structured illumination microscopy. Simultaneous hybridization of FISH probes labeled with different fluorophores enables visualization of multiple sequences at once. Using probes designed specifically to transcribed vs. non-transcribed regions has enabled the simultaneously detect DNA and RNA from the same locus, or from two different loci, in the same FISH assay. The ability to generate high performance FISH probes using chemically synthesized oligo libraries that can simultaneously detect DNA and RNA yields a valuable tool for studies of how localization of specific nucleic acids impacts biological function.

Citation Format: Robert A. Ach, Peter Tsang, Alicia Scheffer-Wong, Laurakay Bruhn, Weston Powell, Jesse Engreitz, Janine LaSalle, Mitchell Guttman, Alice Yamada. Use of complex oligonucleotide libraries for concurrent high-resolution fluorescence imaging of both DNA and RNA in various sample types. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1513. doi:10.1158/1538-7445.AM2014-1513

Predicting walking function of patients one month poststroke using modified Rivermead mobility index on admission

Being able to predict walking ability of patients with stroke at an early stage is useful in formulating realistic rehabilitation goals and facilitating early discharge planning, which are beneficial not only to the patients but their family members and health care providers. This study aimed to use the modified Rivermead mobility index (MRMI) of the stroke patients on day 3 of their admission to predict their independent walking ability on day 28 postadmission. A total of 232 patients with acute stroke who were admitted to the acute hospital were recruited. Fifty-three percent of them (n = 123) were able to achieve independent walking ability after 28 days of admission whereas 47.0% of them (n = 109) failed to do so. The receiver operating characteristics curve analysis was performed. The optimal cutoff score with the highest sum of sensitivity and specificity was found to be 18.5 (sensitivity, 85.0%; specificity, 75.0%) and the area under the curve was .880. In conclusion, MRMI on day 3 of admission maybe useful in predicting independent walking ability 1 month after stroke.

Vignetting-free computer-generated Fresnel holograms by mask shifting

In computer-generated Fresnel holography, direct sampling (DS) and simple shading (SS) are two common ways to generate sampled Fresnel zone plates (FZPs) on the hologram plane. Nevertheless, either aliasing or vignetting, or both, will occur in the reconstructed image when the DS method or the SS method is applied. To avoid vignetting together with aliasing in the two sampling methods, either the object size or the object distance must be restricted in generating the holograms. In this paper we propose a mask-shifting (MS) method to generate the sampled FZPs. The main concept of the MS method is that the center of the FZP can be shifted relative to the center of the mask against the FZP when the FZP is at the margin of the hologram. The shifting of the mask will result in only a phase shift and will not change the intensity distribution of the reconstructed point. Thus, by using the MS method, aliasing and vignetting are simultaneously alleviated in any combination of object size and object distance.

A Prader-Willi locus lncRNA cloud modulates diurnal genes and energy expenditure

Prader–Willi syndrome (PWS), a genetic disorder of obesity, intellectual disability and sleep abnormalities, is caused by loss of non-coding RNAs on paternal chromosome 15q11-q13. The imprinted minimal PWS locus encompasses a long non-coding RNA (lncRNA) transcript processed into multiple SNORD116 small nucleolar RNAs and the spliced exons of the host gene, 116HG. However, both the molecular function and the disease relevance of the spliced lncRNA 116HG are unknown. Here, we show that 116HG forms a subnuclear RNA cloud that co-purifies with the transcriptional activator RBBP5 and active metabolic genes, remains tethered to the site of its transcription and increases in size in post-natal neurons and during sleep. Snord116del mice lacking 116HG exhibited increased energy expenditure corresponding to the dysregulation of diurnally expressed Mtor and circadian genes Clock, Cry1 and Per2. These combined genomic and metabolic analyses demonstrate that 116HG regulates the diurnal energy expenditure of the brain. These novel molecular insights into the energy imbalance in PWS should lead to improved therapies and understanding of lncRNA roles in complex neurodevelopmental and metabolic disorders.

Abstract 4205: Simultaneous high resolution fluorescence imaging of cellular DNA and RNA enabled by complex oligonucleotide libraries in various sample types

Fluorescence in situ Hybridization (FISH) is a powerful technique for determining the structure, organization, and localization of specific nucleic acid sequences within individual cells. However, the use of FISH has often been dependent upon access to cloned template DNA for the generation of probes, which can be difficult if clones for specific regions are unavailable, or if the genomic region of interest contains repetitive and/or other problematic sequences. We have leveraged our ability to chemically synthesize DNA in massively parallel reactions to produce libraries of oligonucleotides up to 200 bases in length that can be used for the generation of FISH probes. The sequences of the oligonucleotides in these libraries are selected in silico using empirically determined criteria so as to avoid repetitive elements or regions homologous to other non-targeted loci. Using oligonucleotide library-derived FISH probes on DNA, human genomic regions as small as 1.8 kb and as large as whole chromosomes can be visualized in both metaphase and interphase cells using the same simple assay protocol. Because of the inherent flexibility in our probe design methods, we readily visualized regions rich in repeats and/or GC content. We have also used these oligonucleotide library-derived FISH probes to detect the localization of a variety of both coding and non-coding RNAs in fixed cells, using both conventional fluorescence and structured illumination microscopy. Simultaneous hybridization of FISH probes labeled with different fluorophores enables visualization of multiple sequences at once. Using probes designed specifically to transcribed vs. non-transcribed regions, we have been able to simultaneously detect DNA and RNA from the same locus in the same FISH assay. We have successfully used this technique in several types of fixed tissue culture cells as well as in formalin-fixed paraffin-embedded tissue sections. Our oligo FISH methods are readily compatible with the co-detection of cellular proteins by immunocytochemistry. The ability to generate high performance FISH probes using chemically synthesized oligo libraries that can work flexibly with co-detection of other molecules yields a valuable tool for studies of how localization of specific nucleic acids impacts biological function.

Citation Format: Robert A. Ach, Peter Tsang, Alicia Scheffer-Wong, Laurakay Bruhn, Weston Powell, Janine LaSalle, Alice Yamada. Simultaneous high resolution fluorescence imaging of cellular DNA and RNA enabled by complex oligonucleotide libraries in various sample types. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4205. doi:10.1158/1538-7445.AM2013-4205

Derivation conditions impact X-inactivation status in female human induced pluripotent stem cells

Female human induced pluripotent stem cell (hiPSC) lines exhibit variability in X-inactivation status. The majority of hiPSC lines maintain one transcriptionally active X (Xa) and one inactive X (Xi) chromosome from donor cells. However, at low frequency, hiPSC lines with two Xas are produced, suggesting that epigenetic alterations of the Xi occur sporadically during reprogramming. We show here that X-inactivation status in female hiPSC lines depends on derivation conditions. hiPSC lines generated by the Kyoto method (retroviral or episomal reprogramming), which uses leukemia inhibitory factor (LIF)-expressing SNL feeders, frequently had two Xas. Early passage Xa/Xi hiPSC lines generated on non-SNL feeders were converted into Xa/Xa hiPSC lines after several passages on SNL feeders, and supplementation with recombinant LIF caused reactivation of some of X-linked genes. Thus, feeders are a significant factor affecting X-inactivation status. The efficient production of Xa/Xa hiPSC lines provides unprecedented opportunities to understand human X-reactivation and -inactivation.

Abstract 2102: High resolution fluorescence imaging of cellular DNA and RNA enabled by the synthesis of complex oligonucleotide libraries

Fluorescence in situ Hybridization (FISH) is a powerful technique for studying the structure, organization, and localization of nucleic acids within individual cells. However, the use of FISH has often been dependent upon access to cloned template DNA for the generation of probes. Clones for specific regions may be unavailable, or the genomic region of interest may contain repetitive and other non-informative sequences which can be problematic for FISH analysis. We have leveraged our ability to chemically synthesize DNA in massively parallel reactions to produce libraries of oligonucleotides up to 200 bases in length that can be used to generate FISH probes. The sequences of the oligonucleotides in these libraries are selected in silico using empirically determined criteria so as to avoid repetitive elements or regions homologous to other non-targeted loci. Using oligonucleotide library-derived FISH probes on DNA, human genomic regions as small as 1.8 kb and as large as whole chromosomes can be visualized in both metaphase and interphase cells using the same simple assay protocol. Because of the inherent flexibility in our probe design methods, we readily visualized regions rich in repeats and/or GC content. Using oligonucleotide library-derived FISH probes on RNA, we have been able to detect the localization of a variety of both coding and non-coding RNAs in fixed cells, using both conventional fluorescence and structured illumination microscopy. Simultaneous hybridization of FISH probes labeled with different fluorophores enables visualization of multiple sequences at once. Using probes designed specifically to transcribed vs. non-transcribed regions, we have been able to simultaneously detect DNA and RNA from the same locus in the same FISH assay. Our oligo FISH methods are readily compatible with the co-detection of cellular proteins by immunocytochemistry. The ability to generate high performance FISH probes using chemically synthesized oligo libraries that can work flexibly with co-detection of other molecules yields a valuable tool for studies of how localization of specific nucleic acids impacts biological function.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2102. doi:1538-7445.AM2012-2102

Complex Fresnel hologram display using a single SLM

We propose a novel optical method to display a complex Fresnel hologram using a single spatial light modulator (SLM). The method consists of a standard coherent image processing system with a sinusoidal grating at the Fourier plane. Two or three position-shifted amplitude holograms displayed at the input plane of the processing system can be coupled via the grating and will be precisely overlapped at the system's output plane. As a result, we can synthesize a complex hologram that is free of the twin image and the zero-order light using a single SLM. Because the twin image is not removed via filtering, the full bandwidth of the SLM can be utilized for displaying on-axis holograms. In addition, the degree of freedom of the synthesized complex hologram display can be extended by involving more than three amplitude holograms.

Low-bit-rate computer-generated color Fresnel holography with compression ratio of over 1600 times using vector quantization [Invited]

We propose a method for compressing a digital color Fresnel hologram based on vector quantization (VQ). The complex color hologram is first separated into three complex holograms, each representing one of the primary colors. Subsequently, each hologram is converted into what we call a real Fresnel hologram and compressed with VQ based on a universal codebook. Experimental evaluation reveals that our scheme is capable of attaining a compression ratio of over 1600 times and still preserving acceptable visual quality on the reconstructed images. Moreover, the decoding process is free from computation and highly resistant to noise contamination on the compressed data.

Holographic video at 40 frames per second for 4-million object points

We propose a fast method for generating digital Fresnel holograms based on an interpolated wavefront-recording plane (IWRP) approach. Our method can be divided into two stages. First, a small, virtual IWRP is derived in a computational-free manner. Second, the IWRP is expanded into a Fresnel hologram with a pair of fast Fourier transform processes, which are realized with the graphic processing unit (GPU). We demonstrate state-of-the-art experimental results, capable of generating a 2048 x 2048 Fresnel hologram of around 4 × 10(6) object points at a rate of over 40 frames per second.

Abstract 3880: Synthesis of complex oligonucleotide libraries enables flexible and precise high-resolution fluorescence imaging of cellular nucleic acids

Fluorescence in situ Hybridization (FISH) is a powerful technique for studying chromosome structure, organization, and stability. To date, the use of FISH has been largely dependent upon access to cloned template DNA for the generation of probes. Clones for specific regions may be unavailable, or the genomic region of interest may contain repetitive and other non-informative sequences which can be problematic for FISH analysis. We have leveraged our ability to chemically synthesize DNA in massively parallel reactions to produce libraries of oligonucleotides up to 200 bases in length that can be used to generate FISH probes. The sequences of the oligonucleotides in these libraries are selected in silico using empirically determined criteria so as to avoid repetitive elements or regions homologous to other non-targeted loci, thus targeting only the most informative elements in the region of the genome to be analyzed. We demonstrate that using our FISH technique, human genomic regions as small as 1.8 kb and as large as whole chromosomes can be visualized in both metaphase and interphase cells using the same simple assay protocol. In addition, specific and robust signals can readily be obtained for chromosomal regions rich in repeats and/or GC content. These libraries can also be used to determine the localization of cellular RNAs. Co-detection of both nuclear proteins by immunocytochemistry and fluorescent imaging of chromosome domains has also been demonstrated.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3880. doi:10.1158/1538-7445.AM2011-3880

Population-genetic properties of differentiated human copy-number polymorphisms

Copy-number variants (CNVs) can reach appreciable frequencies in the human population, and recent discoveries have shown that several of these copy-number polymorphisms (CNPs) are associated with human diseases, including lupus, psoriasis, Crohn disease, and obesity. Despite new advances, significant biases remain in terms of CNP discovery and genotyping. We developed a method based on single-channel intensity data and benchmarked against copy numbers determined from sequencing read depth to successfully obtain CNP genotypes for 1495 CNPs from 487 human DNA samples of diverse ethnic backgrounds. This microarray contained CNPs in segmental duplication-rich regions and insertions of sequences not represented in the reference genome assembly or on standard SNP microarray platforms. We observe that CNPs in segmental duplications are more likely to be population differentiated than CNPs in unique regions (p = 0.015) and that biallelic CNPs show greater stratification when compared to frequency-matched SNPs (p = 0.0026). Although biallelic CNPs show a strong correlation of copy number with flanking SNP genotypes, the majority of multicopy CNPs do not (40% with r > 0.8). We selected a subset of CNPs for further characterization in 1876 additional samples from 62 populations; this revealed striking population-differentiated structural variants in genes of clinical significance such as OCLN, a tight junction protein involved in hepatitis C viral entry. Our microarray design allows these variants to be rapidly tested for disease association and our results suggest that CNPs (especially those that cannot be imputed from SNP genotypes) might have contributed disproportionately to human diversity and selection.

Computer generation of binary Fresnel holography

Binarization of Fresnel holograms by direct thresholding based on the polarity of the fringe pattern is studied. It is found that if the hologram is binarized (i.e., for black and white hologram pixels) in this manner, only the edges of the object are preserved in the reconstructed image. To alleviate the errors caused by binarization, the use of error diffusion has been routinely employed. However, the reconstructed image using such standard technique is heavily contaminated with random noise. In this paper, we propose a novel noniterative method for generating Fresnel holograms that are suitable for binarization. Our method is capable of preserving good visual quality on the reconstructed images.

Visualization of fine-scale genomic structure by oligonucleotide-based high-resolution FISH

The discovery of complex structural variations that exist within individual genomes has prompted a need to visualize chromosomes at a higher resolution than previously possible. To address this concern, we established a robust, high-resolution fluorescence in situ hybridization (FISH) method that utilizes probes derived from high complexity libraries of long oligonucleotides (>150 mers) synthesized in massively parallel reactions. In silico selected oligonucleotides, targeted to only the most informative elements in 18 genomic regions of interest, eliminated the need for suppressive hybridization reagents. Because of the inherent flexibility in our probe design methods, we readily visualized regions as small as 6.7 kb with high specificity on human metaphase chromosomes, resulting in an overall success rate of 94%. Two-color FISH over a 479-kb duplication, initially reported as being identical in 2 individuals, revealed distinct 2-color patterns representing direct and inverted duplicons, demonstrating that visualization by high-resolution FISH provides further insight in the fine-scale complexity of genomic structures. The ability to design FISH probes for any sequenced genome along with the ease, reproducibility, and high level of accuracy of this technique suggests that it will be powerful for routine analysis of previously difficult genomic regions and structures.

Array comparative genomic hybridization of peripheral blood granulocytes of patients with myelodysplastic syndrome detects karyotypic abnormalities

The diagnosis of myelodysplastic syndromes (MDSs) relies largely on morphologic and karyotypic abnormalities, present in about 50% of patients with MDS. Array-based genomic platforms have identified copy number alterations in 50% to 70% of bone marrow samples of patients with MDS with a normal karyotype, suggesting a diagnostic role for these platforms. We investigated whether blood granulocytes harbor the same copy number alterations as the marrow of affected patients. Of 11 patients, 4 had cytogenetic abnormalities shown by conventional karyotyping involving chromosomes 5, 8, 11, 20, and X, and these changes were seen in the granulocytes of all 4 patients by using array comparative genomic hybridization (aCGH). Cryptic alterations were identified at a significantly higher level in marrow CD34+ cells compared with granulocytes (P < .0001). These data suggest that aCGH analysis of circulating granulocytes may be useful in detecting gross karyotypic alterations in patients with MDS when marrow examination has failed or not been done.

Abstract 328: Complex oligonucleotide libraries enable high-resolution cytogenetic analysis of human and mouse genomes with fluorescence in situ hybridization (FISH)

Cytogenetic analysis of chromosomes using Fluorescence in situ Hybridization (FISH) is a powerful method for the study of chromosome structure, organization, and stability. However, to date, the utility of FISH has largely depended upon access to cloned template DNA used to generate probes. Clones for specific regions are often unavailable, or the genomic template may contain repetitive and other non-informative sequences which can confound FISH analysis. We have leveraged our ability to chemically synthesize oligonucleotides in massively parallel reactions to produce DNA libraries that can be used to generate FISH probes. The sequences of the oligonucleotides in these libraries are selected in silico using empirically determined criteria so as to target only the most informative elements in the genomic region to be analyzed and avoiding any repetitive elements or regions homologous to other non-targeted loci. Our FISH protocol is similar to ones used for FISH with BAC probes. Using our methods, human chromosomal regions as small as 1.8 kb and as large as chromosome arms were successfully visualized in both metaphase and interphase cells. Using our probe design methods, we readily obtained specific and robust signals for chromosomal regions rich in repeats and/or GC content.

We also investigated the utility of these probes for studies of mouse chromosomes by generating probes for over ten loci in the mouse genome. All the probes hybridized well using cytologic and cryosectioned samples. In addition, FFPE samples showed promising preliminary results. We have also applied our FISH methods to develop chromosome-specific enumeration probes for the mouse genome at pericentromeric regions. These enumeration probes should be useful for detecting aneuploidies, polyploidies, and other genomic rearrangements that were previously difficult to study at single-cell resolution, particularly in tissue samples. Successful co-hybridization of chromosome enumeration probes and loci-specific probes in mouse intestinal crypt cells allowed for accurate copy number analyses in tissue samples. We are also continuing to explore other breakthrough applications that are enabled by our oligonucleotide-based FISH methodology.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 328.

Fast generation of Fresnel holograms based on multirate filtering

One of the major problems in computer-generated holography is the high computation cost involved for the calculation of fringe patterns. Recently, the problem has been addressed by imposing a horizontal parallax only constraint whereby the process can be simplified to the computation of one-dimensional sublines, each representing a scan plane of the object scene. Subsequently the sublines can be expanded to a two-dimensional hologram through multiplication with a reference signal. Furthermore, economical hardware is available with which sublines can be generated in a computationally free manner with high throughput of approximately 100 M pixels/second. Apart from decreasing the computation loading, the sublines can be treated as intermediate data that can be compressed by simply downsampling the number of sublines. Despite these favorable features, the method is suitable only for the generation of white light (rainbow) holograms, and the resolution of the reconstructed image is inferior to the classical Fresnel hologram. We propose to generate holograms from one-dimensional sublines so that the above-mentioned problems can be alleviated. However, such an approach also leads to a substantial increase in computation loading. To overcome this problem we encapsulated the conversion of sublines to holograms as a multirate filtering process and implemented the latter by use of a fast Fourier transform. Evaluation reveals that, for holograms of moderate size, our method is capable of operating 40,000 times faster than the calculation of Fresnel holograms based on the precomputed table lookup method. Although there is no relative vertical parallax between object points at different distance planes, a global vertical parallax is preserved for the object scene as a whole and the reconstructed image can be observed easily.

Benign copy number changes in clinical cytogenetic diagnostics by array CGH

A database of apparently benign copy number variants (bCNVs) detected by a Spectral Genomics Inc./PerkinElmer BAC array platform has been maintained through the University of Utah Comparative Genomic Hybridization laboratory since 2005. The target population for this database represents 1,275 patients with abnormal phenotypes, primarily children referred for developmental delay and mental retardation. These bCNVs are independent of any identified copy number abnormality detected. The most common 35 bCNVs observed and their frequencies are reported here, and a subset of ten of the patients studied was evaluated on a new oligonucleotide CNV array set designed by Agilent Technologies. There was a 76% concordance of calls for these 35 bCNVs detected by both array platforms in the same patients. The higher resolution of the Agilent oligonucleotide array compared to the BAC array allowed determination of the precise breakpoints of the observed CNVs, in addition to documentation of additional CNVs of smaller sizes. As expected, observed CNVs and their frequencies were generally consistent with those of other previously published and available databases, including the Database of Genomic Variants (http://projects.tcag.ca/variation/). The availability of these data should assist other clinical laboratories in the evaluation of CNVs of unknown clinical significance.

Triple negative status as a risk factor for the development of brain metastases in African American breast cancer patients

Abstract #2093

Background: Previous studies have described triple negative (TN) breast cancer (ER/PR/ HER2/neu negative) as an aggressive and poor prognostic phenotype with higher relapse rate (RR), distant RR, and shorter survival. The incidence of TN breast cancer has reportedly been higher (30-35%) in African American (AA) women compared to the general population (15%) but the clinical outcomes of TN patients (pts) who develop brain metastases compared to the non-triple negative (NTN) group has not been well described.&#x2028; Methods: We retrospectively reviewed tumor registry data from a large academic medical center serving an inner city population. A total of 282 AA women with invasive breast cancer were identified from 1994-2006 and 248 were determined to be in stages I-III. Characteristics evaluated include age, TNM stage at diagnosis, ER, PR, Her2/neu status, and grade. The RR, distant RR, rate of brain metastases, time from diagnosis to brain metastases, and overall survival were determined.&#x2028; Results: The incidence of TN disease in AA women was 30% (82/282). Median age (57 yrs) was similar in both TN and NTN groups. With a median follow-up of 5.5 years, the RR (30% vs. 14%; p=0.02) and distant RR (22% vs. 10%; p=0.02) were higher for the TN vs. NTN group. Six of 72 (9%) TN pts developed brain metastases compare to 6/178 (3%) in NTN group. There was a shorter time to development of brain metastases (1.7 vs. 6.1; p=0.01) and a lower survival time after brain metastases (0.6 yrs vs. 1.6 yrs) in the TN vs. NTN group.&#x2028; &#x2028; Conclusion: This study represents one of the largest reported series of AA women with breast cancer. TN pts are at higher risk of developing brain metastases. Not only the time to develop brain metastases was shorter but overall survival after development of brain metastases remained poor in TN group compared to NTN group. TN status should be considered as an independent risk factor for the development of brain metastases.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2093.

Mapping and sequencing of structural variation from eight human genomes

Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale--particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects.

The fine-scale and complex architecture of human copy-number variation

Despite considerable excitement over the potential functional significance of copy-number variants (CNVs), we still lack knowledge of the fine-scale architecture of the large majority of CNV regions in the human genome. In this study, we used a high-resolution array-based comparative genomic hybridization (aCGH) platform that targeted known CNV regions of the human genome at approximately 1 kb resolution to interrogate the genomic DNAs of 30 individuals from four HapMap populations. Our results revealed that 1020 of 1153 CNV loci (88%) were actually smaller in size than what is recorded in the Database of Genomic Variants based on previously published studies. A reduction in size of more than 50% was observed for 876 CNV regions (76%). We conclude that the total genomic content of currently known common human CNVs is likely smaller than previously thought. In addition, approximately 8% of the CNV regions observed in multiple individuals exhibited genomic architectural complexity in the form of smaller CNVs within larger ones and CNVs with interindividual variation in breakpoints. Future association studies that aim to capture the potential influences of CNVs on disease phenotypes will need to consider how to best ascertain this previously uncharacterized complexity.

Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: implications for association studies of complex diseases

The discovery of copy number variation in healthy individuals is far from complete, and owing to the resolution of detection systems used, the majority of loci reported so far are relatively large ( approximately 65%>10 kb). Applying a two-stage high-resolution array comparative genomic hybridization approach to analyse 50 healthy Caucasian males from northern France, we discovered 2208 copy number variants (CNVs) detected by more than one consecutive probe. These clustered into 1469 CNV regions (CNVRs), of which 721 are thought to be novel. The majority of these are small (median size 4.4 kb) and most have common boundaries, with a coefficient of variation less than 0.1 for 83% of endpoints in those observed in multiple samples. Only 6% of the CNVRs analysed showed evidence of both copy number losses and gains at the same site. A further 6089 variants were detected by single probes: 48% of these were observed in more than one individual. In total, 2570 genes were seen to intersect variants: 1284 in novel loci. Genes involved in differentiation and development were significantly over-represented and approximately half of the genes identified feature in the Online Mendelian Inheritance in Man database. The biological importance of many genes affected, along with the well-conserved nature of the majority of the CNVs, suggests that they could have important implications for phenotype and, thus, be useful for association studies of complex diseases.

Construction of a counterselection-based in-frame deletion system for genetic studies of Streptococcus mutans

Genetic studies of Streptococcus mutans have benefited greatly from the numerous techniques that have been successfully adapted for use in this organism. One notable exception is the lack of a negative selection system that can be employed for the easy isolation of markerless in-frame deletions. In this study, we report the development of a galK/galactose-based negative selection system in S. mutans for this purpose. This system consists of a recipient strain (IFD140) that contains a deletion in the galKTE operon and a suicide vector (pIFD-Sm) that carries the S. mutans galK open reading frame fused to the constitutive lactate dehydrogenase (ldh) promoter. Using this system we created a markerless in-frame deletion in the beta-galactosidase (lacG) gene within the S. mutans lactose operon. After vector integration, plasmid excision after counterselection appeared to have occurred in 100% of the galactose-resistant colonies and resulted in in-frame deletions in 50% of the screened isolates. Based on the ratio of galactose-resistant cells to total cells, we determined that plasmid excision occurred at a frequency of approximately 1/3000 cells. Furthermore, the simplicity of this system should make it adaptable for use in numerous other gram-positive and gram-negative organisms.

Clonal T-Large Granular Lymphocyte Proliferation in Solid Organ Transplant Recipients

Large granular lymphocytic (LGL) leukemia is a rare disorder, usually caused by clonal proliferation of CD3+ CD57+ T-LGL cells. T-cell clonality is confirmed by rearrangements of the T-cell receptor (TCR) gene. Characteristic features of T-LGL leukemia include neutropenia, anemia, and constitutional symptoms such as fatigue. Many solid organ transplant recipients experience similar symptoms and have neutropenia and anemia often attributed to immunosuppressive therapy. The purpose of this study was to determine the prevalence of T-LGL proliferation in solid organ transplant recipients and demonstrate its association with leukopenia and anemia. Twenty-three cardiac and renal transplant patients were evaluated by peripheral smear examination, flow cytometry, and TCR gene rearrangement study by polymerase chain reaction. Ten of 14 (71%) cardiac transplant patients and 4 of 9 (44%) renal transplant patients, without evidence of either allograft rejection or a viral syndrome, were found to have clonal expansion of T-LGL cells. Constitutional symptoms were present in 30% of these patients. Anemia of <10 g/dL was seen in 75% of renal transplant and 10% of cardiac transplant patients. None of these patients had significant neutropenia defined as absolute neutrophil count of 1500 mu/L. Most of the patients did not require any specific therapeutic intervention. Although TCR gene rearrangement is considered a hallmark of T-LGL leukemia, we believe that this monoclonality is not a true form of posttransplant lymphoproliferative disorder. Constant antigenic stimulus from the allograft may be the underlying etiology of clonal expansion and may contribute to cytopenias and fatigue seen in transplant patients.

Intravenous immunoglobulin in antiphospholipid syndrome and maternal floor infarction when standard treatment fails: a case report

Obstetrical antiphospholipid syndrome (APS) is associated with maternal and fetal morbidity and mortality. Standard treatment with low-dose acetylsalicylic acid and unfractionated heparin has achieved up to a 70 to 80% likelihood of success. Conversely, up to 30% of women with APS will have further pregnancy losses, despite treatment. Intravenous immunoglobulin (IVIG) may be a promising adjuvant when standard treatment fails. We present a case of a 35-year-old woman with obstetrical APS and maternal floor infarction in prior pregnancy losses who continued to have further unsuccessful pregnancies despite standard treatment with acetylsalicylic acid and unfractionated heparin. On an investigational basis, she was prescribed concomitant IVIG and had two subsequent healthy newborns. IVIG appears to be promising in obstetrical patients with APS who are refractory to standard treatment. Prior history of maternal floor infarction may be a prognostic indicator for triple therapy for obstetrical APS.

Hereditary Angioedema Managed with Low-Dose Danazol and C1 Esterase Inhibitor Concentrate: A Case Report

BACKGROUND

Hereditary angioedema (HAE) is a rare life-threatening disease that can occur in pregnancy.

CASE

A nulliparous woman was diagnosed as having HAE at 22 weeks of gestation after a series of symptomatic episodes. Following an initial course of C1 esterase inhibitor (C1EI) therapy for an acute episode of HAE, she was treated with danazol for prophylaxis. Danazol did not prevent recurrence of symptoms, its use was discontinued after six weeks. Thereafter, the patient was treated exclusively with C1EI at weekly intervals for exacerbations of her HAE. At 37 weeks' gestation, she delivered healthy 3050 g female neonate. At the time of discharge the female neonate had no signs of virilization or congenital anomalies.

CONCLUSION

Low dose danazol was ineffective in treating this woman's HAE in pregnancy. The use of C1EI in pregnancy is associated with good outcomes.

Severe periodontitis in a 5-year-old girl with hyperimmunoglobulin E syndrome

The hyperimmunoglobulin E syndrome (HIES) is a multisystem disorder that affects the: (1) dentition; (2) skeleton; (3) connective tissues; and (4) immune system. Little is known about periodontal manifestations of the syndrome. The purpose of this report was to describe a 5-year-old girl with suspected autosomal-recessive HIES syndrome who revealed profusely bleeding and painful gingiva and generalized aggressive periodontitis. A polymerase chain reaction (PCR)-based microbiological examination detected Porphyromonas gingivalis, Tannerella forsythia, Prevotella nigrescens, Treponema denticola, Eikenella corrodens, and Campylobacter rectus in the deep periodontitis lesions. The extraction of all deciduous teeth due to a poor prognosis and risk of systemic infection led to resolution of the oral inflammation. Long-term follow-up is required to determine the periodontal prognosis of the erupting permanent teeth.

Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA

Array-based comparative genomic hybridization (CGH) measures copy-number variations at multiple loci simultaneously, providing an important tool for studying cancer and developmental disorders and for developing diagnostic and therapeutic targets. Arrays for CGH based on PCR products representing assemblies of BAC or cDNA clones typically require maintenance, propagation, replication, and verification of large clone sets. Furthermore, it is difficult to control the specificity of the hybridization to the complex sequences that are present in each feature of such arrays. To develop a more robust and flexible platform, we created probe-design methods and assay protocols that make oligonucleotide microarrays synthesized in situ by inkjet technology compatible with array-based comparative genomic hybridization applications employing samples of total genomic DNA. Hybridization of a series of cell lines with variable numbers of X chromosomes to arrays designed for CGH measurements gave median ratios for X-chromosome probes within 6% of the theoretical values (0.5 for XY/XX, 1.0 for XX/XX, 1.4 for XXX/XX, 2.1 for XXXX/XX, and 2.6 for XXXXX/XX). Furthermore, these arrays detected and mapped regions of single-copy losses, homozygous deletions, and amplicons of various sizes in different model systems, including diploid cells with a chromosomal breakpoint that has been mapped and sequenced to a precise nucleotide and tumor cell lines with highly variable regions of gains and losses. Our results demonstrate that oligonucleotide arrays designed for CGH provide a robust and precise platform for detecting chromosomal alterations throughout a genome with high sensitivity even when using full-complexity genomic samples.

Treatment of antiphospholipid antibody syndrome (APS) in pregnancy: a randomized pilot trial comparing low molecular weight heparin to unfractionated heparin

OBJECTIVE

To compare low molecular weight heparin (LMWH), specifically dalteparin, to unfractionated heparin (UFH) for the treatment of antiphospholipid antibody syndrome (APS) in pregnancy.

METHODS

In a tertiary referral centre, 28 women met the 1999 International Consensus Criteria for APS, based on their obstetrical history and APS serology. The women were randomized, using a random numbers table with blocks of 12, to receive either prophylactic dosing of dalteparin or UFH starting either preconceptionally or early in pregnancy. All women also received low-dose acetylsalicylic acid, started preconceptionally. The primary outcome was a live birth. The secondary outcomes were maternal and fetal complications.

RESULTS

Of the 14 women who received the LMWH, dalteparin, and the 14 women who received UFH, 1 woman in each group did not conceive. Nine of the 13 women (69%) given dalteparin had a successful pregnancy (95% confidence interval [CI], 39-91%), compared to 4 out of the 13 women (31%) in the UFH group (95% CI, 9-61%). Nine women in total had spinal or epidural anaesthesia, and there were no complications overall.

CONCLUSION

Dalteparin may be an effective alternative to UFH for treatment of APS in pregnancy. A multicentre randomized trial is needed to determine benefit-to-risk ratios for the use of dalteparin and UFH to treat this high-risk obstetrical condition. Pharmacokinetic and pharmacodynamic studies are also recommended to maximize therapeutic response and minimize toxicity.

Universal prestorage leukoreduction in Canada decreases platelet alloimmunization and refractoriness

Randomized controlled trials have shown a reduction in platelet alloimmunization and refractoriness in patients with acute leukemia (AL) with the use of poststorage leukoreduction of blood products. Universal prestorage leukoreduction (ULR) of red cell and platelet products has been performed in Canada since August 1999. We conducted a retrospective analysis of 13 902 platelet transfusions in 617 patients undergoing chemotherapy (CT) for AL or stem cell transplantation (SCT) before (n = 315) and after (n = 302) the introduction of ULR. Alloimmunization was significantly reduced (19% to 7%, P <.001) in the post-ULR group. Alloimmune platelet refractoriness was similarly reduced (14% to 4%, P <.001). Fewer patients in the post-ULR group received HLA-matched platelets (14% vs 5%, P <.001). Alloimmunization and alloimmune refractoriness in the 318 patients who were previously pregnant and/or transfused were also reduced after ULR (P =.023 and P =.005, respectively). In a Cox regression model, the 3 independent factors that predicted for alloimmune refractoriness were nonleukoreduced blood products (relative risk [RR], 2.2 [95% CI, 1.2-4.3]), a history of pregnancy and/or transfusion (RR, 2.3 [95% CI, 1.3-4.2]), and receipt of 13 or more platelet transfusions (RR, 6.0 [95% CI, 2.4-15.3]). In conclusion, ULR reduces alloimmunization, refractoriness, and requirements for HLA-matched platelets when applied as routine transfusion practice to patients receiving CT or SCT.

The effect of factor V Leiden carriage on maternal and fetal health

Factor V Leiden is a common genetic mutation that predisposes its carriers to venous thromboembolism. When combined with the hypercoagulable state that is characteristic of pregnancy, there is an increased risk of severe and recurrent pregnancy complications. Factor V Leiden is the most common cause of primary and recurrent venous thromboembolism in pregnancy. Factor V Leiden carriage has consistently been shown to increase the risk of early onset gestational hypertension and HELLP syndrome (Hemolysis, Elevated Liver enzymes, Low Platelets) in pregnancy. Maternal carriage of factor V Leiden is also associated with severe placental abruption and fetal growth disturbances. Although it is unclear whether factor V Leiden causes an increased risk of first trimester miscarriage, it is associated with stillbirth and placental infarction. Patients with venous thromboembolism or severe pregnancy complications should be tested for factor V Leiden and other inherited and acquired thrombophilia. Therapeutic heparin is required for acute thromboembolic events in pregnancy. Patients with factor V Leiden and a previous venous thromboembolism may, according to their level of risk, be offered either prophylactic or therapeutic heparin. The role of antithrombotic therapy in the prevention of severe pregnancy complications remains unclear.

Obstetric implications of the factor V leiden mutation: a review

Factor V Leiden (FVL) is a newly discovered genetic mutation that impairs one of the body's naturally occurring anticoagulation systems. The result is resistance to activated protein C and a predisposition to thrombosis. FVL is the most common cause of primary and recurrent venous thromboembolism in the pregnant and nonpregnant state. The FVL gene is common in the general population and transmitted in an autosomal dominant fashion. When FVL is combined with the prothrombotic state of pregnancy, the result is an increased propensity to manifest a number of pregnancy complications. These include recurrent pregnancy loss and stillbirth, severe and early-onset preeclampsia, placental abruption and possibly, intrauterine growth restriction. It remains unknown whether thromboprophylaxis is effective in ameliorating these pregnancy complications. The current literature and management recommendations are highlighted in this article.

Low incidence of HPV DNA in sera of pretreatment cervical cancer patients

OBJECTIVE

The aim of this study was to investigate the feasibility of using DNA in the circulation as a diagnostic tool for cervical cancer.

METHODS

We used PCR followed by Southern hybridization to detect human papillomavirus (HPV) DNA in serum samples taken from patients of cervical cancer before treatment.

RESULTS

A total of 60 samples were analyzed. In a set of 40 samples, without knowledge of the HPV DNA status in the corresponding cervical carcinomas, we could detect 8 (20%) positive samples, of which 7 (17.5%) were HPV 16 and 1 (2.5%) was HPV 18. In another set of 20 samples, known to be HPV 16 infected in the corresponding cervical carcinomas, we detected only 4 (20%) HPV-16-positive samples. The occurrence of HPV DNA in sera of cervical cancer patients seems sporadic.

CONCLUSION

The low incidence indicates that serum HPV DNA has limited application in the diagnosis of cervical cancer.

The binding of a glycoprotein 120 V3 loop peptide to HIV-1 neutralizing antibodies. Structural implications

The structural and antigenic properties of a peptide ("CRK") derived from the V3 loop of HIV-1 gp120 protein were studied using NMR and SPR techniques. The sequence of CRK corresponds to the central portion of the V3 loop containing the highly conserved "GPGR" residue sequence. Although the biological significance of this conserved sequence is unknown, the adoption of conserved secondary structure (type II beta-turn) in this region has been proposed. The tendency of CRK (while free or conjugated to protein), to adopt such structure and the influence of such structure upon CRK antigenicity were investigated by NMR and SPR, respectively. Regardless of conjugation, CRK is conformationally averaged in solution but a weak tendency of the CRK "GPGR" residues to adopt a beta-turn conformation was observed after conjugation. The influence of GPGR structure upon CRK antigenicity was investigated by measuring the affinities of two cognate antibodies: "5023A" and "5025A," for CRK, protein-conjugated CRK and gp120 protein. Each antibody bound to all the antigens with nearly the same affinity. From these data, it appears that: (a) antibody binding most likely involves an induced fit of the peptide and (b) the gp120 V3 loop is probably conformationally heterogeneous. Since 5023A and 5025A are HIV-1 neutralizing antibodies, neutralization in these cases appears to be independent of adopted GPGR beta-turn structure.

A distinctive composite lymphoma consisting of clonally related mantle cell lymphoma and follicle center cell lymphoma

Although follicle center cell lymphoma and mantle cell lymphoma are both B cell non-Hodgkin's lymphomas (NHL), they are regarded as separate entities with distinct clinical, morphological, immunophenotypic and molecular characteristics. To our knowledge, the coexistence of these 2 lymphomas in the same patient has never been reported. We describe a 70-year-old woman with a long-standing history of follicle center cell lymphoma, cytological grade I, who subsequently developed a composite lymphoma consisting of well-demarcated foci of persistent follicle center cell lymphoma surrounded by mantle cell lymphoma. This morphological interpretation was supported by the presence of both bcl-1 and bcl-2 gene rearrangements, which are molecular genetic hallmarks of mantle cell lymphoma and follicle center cell lymphoma, respectively. Polymerase chain reaction (PCR) analysis for rearranged immunoglobulin heavy chain (IgH) genes showed a dominant band identical in size in microdissected tumor cells of the follicle center cell and mantle cell lymphomas. Cloning and sequence analysis of the PCR products revealed a common clone-specific IgH gene rearrangement in these 2 lymphomas. These findings suggest that this composite lymphoma represents the unusual evolution of a malignant B-cell clone that resulted in the development of 2 morphologically distinct but clonally related B-cell NHLs. These findings also show the importance of integrating morphological, immunophenotypic, and molecular data to enhance our understanding of the complex pathogenic interrelationships in lymphomagenesis.